Geonovast

There's a button on the upper-right of the screen with a hammer and a wrench.  Click on that, and it will pop out a small window.  On there, click "Edit Action Groups"
This will pause the game and let you configure the action groups like you would in the VAB/SPH.

You may have accidentally toggled it off.  Try pressing F4 to toggle it back on.

If you can get a rescue craft to him that has an Engineer, they could EVA over to the pod and use the orbital construction feature to either attach a docking port to the pod, or to remove the parachute that's covering up the hatch.  You could then dock to the pod with the rescue craft or EVA Jeb over, respectively.
Also, welcome aboard, @Gradonius!

Mk2 pod can survive re-entry from Minmus with a 1.25m heat shield, just use the translate tool to pull it out of the pod when you attach it.  It can even survive with no heat shield, although it does get a little toastier.
While it looks silly, you can still send an Mk2 pod up on a 1.25 meter stack.
\
 
Also, a couple side notes for missions like this, since you ran so low on dV.
There's two things you can do on a craft like that (assuming you didn't already) that aren't very obvious.
That pod has some Monopropellent in it.  If you're not using any RCS, then you don't need it!  Empty it out in the VAB.  Less weight = moar dV. Similar thing applies to your heat shield.  They're ablative, so the less ablator they have, the less they weigh.  You could probably knock it down from 200 to 40 or 60 in the VAB for even more weight savings.  

It allows you to change the root part of the craft.
The craft files are organized in a tree structure.  By default, your root part will be the first one you select when starting to build a new craft.  As you attach more parts, they will be added to the tree.  Each part will have exactly one part above it (except the root part) called the parent, and can have any number of parts below it (called children).  This is why, when you grab a part in the middle of your craft and pull it off to the side, more than just the one part is moved.  All the parts that are under that one in the tree go with it.
The re-root tool allows you to change which part is the root.  This is typically used when dealing with subassemblies and merging crafts and not needed when building a one-off rocket or using the stock crafts.

One of the tools will always be active, so to disengage one of them you will just need to click on another. 
Place is just the mode to grab more parts from the left side of the screen and place them onto your ship.
If you have Rotate or Move selected, you can also go back to Place by just grabbing another part to put on the craft.
 

It could be, but the biggest issue seems to be your control point.  See how your navball is completely brown when you take off?  That means that the control point, or the direction your craft is "looking" is pointing straight at the ground.
Right click on the docking port on top and push the button for "Control From Here".  The navball should turn mostly blue, then try again.

Welcome to the forums, @JaxonFranssen2007!
The inflatable port will connect with other inflatable ports, as well as the Clamp-O-Tron Jr.  Nothing else, unfortunately.
Its size is deceptive, I know.  It confused a lot of us when Making History was released.

You can do it with the probe core, if it has one.
If it's just debris, you can rename them or destroy them in the tracking station.  (not my pic)

Are you waiting the full 10 seconds?  The orbit line will disappear once you're within tolerance, but the contract won't complete until you have fulfilled the "maintain stability for 10 seconds" aspect.

Welcome to the forum, @Crystalking8!
There are two types of antenna in the game: Direct and Relay.
The DTS-M1 is not a relay antenna.
In order to bounce a signal through a satellite, the satellite you're going through must have a relay antenna on board. 
This wiki page will show you all the antennas in the stock game, and which ones are relays.  https://wiki.kerbalspaceprogram.com/wiki/Antenna

There is something you can do.  The game automatically backs up your game periodically.  Inside the save's folder, there's another folder called Backup, which saves the last 5 auto backups.  You can copy any of these to the parent folder, and then load that game from the Load Game function in the game.  Or, you can name it persistent.sfs and the game will load it automatically when you open that save in the game.
How did you delete it?  From inside the game or did you delete the folder manually?  If you did it manually, it may still be in your Trash.

The Re-root tool will be your friend here.
When you merge in a craft, you can only attach it by way of its root part.  Either change the root of to where you want to attach it from and save the craft before merging it in, or use the re-root tool on it after you've merged it.  The re-root tool is up by the translate and rotate buttons.

It sounds like you have the decoupler backwards.  Do you have any screenshots you can share?

Same Vessel Interaction: By default, parts of the same ship cannot interact with each other.  As far as I'm aware, this was done so that clipping parts into one another during assembly didn't cause 'splody issues in flight.  Now, however, all parts with this setting on will interact with each other.  This can be quite handy if you're doing stuff with the newish robotic pieces.
Rigid Attachment: Something about the strength of the attachment between the part and its parent.  Can make it stronger, but can also make it more brittle in certain situations.
First Hop Distance: I'm not sure why that's there, actually.  I don't think it's much use for anything.
Deploy Shielded: Parts, like struts and landing gear, by default will not deploy if the game believes they are within a cargo bay.  This is troublesome, especially on large planes, because sometimes the game considers them inside the bay even when they're attached to the outside.  If you need to make sure the gear will always deploy when there's a chance it's partially inside a cargo bay, turn this on.
 
Fairings:
Sides: Exactly as it seems, sets the number of sides, or slices of the fairing.  This, in my experience, is mostly and aesthetic thing, although upping the number of sides can be helpful if the fairing pieces hit your payload on deploy.
Clamshell Deploy: With this off, all the sides of your fairing will deploy into multiple pieces, like confetti.  With this on, each side will remain one piece when deployed, like real fairings.  I like to put this on, but it can cause issues if the fairing is too close to the payload near the fairing base.
Next two I'll do in reverse order:
Interstage Nodes: When you turn this on, you'll see that there are now multiple stack attach nodes above the fairing base.  This allows you to stack multiple payloads in a fairing without them touching.
Truss Structure: When you have Interstage Nodes on, and attach something to one of the new nodes, a plate and side supports will appear between the base and the node you used.  These are strictly for looks and don't actually do anything.  You can turn the visual-only supports off with this option.

I'm not having any problem.



Of course it's hard to get screenshots of this thing exactly where it's lining up, but this one really doesn't have any clipping.

No.
When you switch away from a vessel the game sticks the vessel onto rails.  This means that the only calculations done for its trajectory are the ones related to gravity.  Each planet also has an "auto-delete" altitude, which means that any vessel that's on rails and falls under that altitude will be automatically delete.  The game will consider it destroyed and any crew on board will be killed.
The game has what's called a "physics bubble".  Your selected craft, and any other crafts within that bubble will have the physics calculations done for them, which is required for the parachutes to work.  So you would have to follow your pods down fairly closely with another craft to get them to work.
I'm not sure if the Stage Recovery mod would help in this situation.
Also I'm moving this to Gameplay Questions.

Moved to Gameplay Questions.
Welcome to the forum, @~SYSTEM~.  I never found much use for the in-game tutorials.  They seem to be really good for telling you how to not do things.
Someone should be along shortly to provide more detailed help!  Good luck!

If you have one in flight, you can retrieve it that way with a special tool.
Although, there is a bit of a "lifehack (I guess)" for this that I discovered by accident.
If you have a period in the craft name, it will ask for confirmation every time you try to save it.

The Squad and SquadExpansion folders are not mods.  They're the stock game.
The 1.8 update is going to break a lot of mods.
I would move the Squad and SquadExpansion folders back in.  Then do a file validation with Steam.  Make sure it works stock, then add the mods back one by one and see if they work.
I also see you have a "GameData" folder in your list.  This is pretty atypical and likely indicates a mod installed incorrectly.
Since your core issue seems to be mod related, I'm moving this to the modded tech support subforum.

I've noticed that in 1.7.3, when you use the re-root tool, you actually have to click on the ship's root part in order to re-root, when before, you could just click anywhere.

I think I might see the problem with a NearFutureConstruction patch.  It appears that it's destroying the stock mesh.  I believe this is because it replaces it with a switchable mesh.
Can you try temporarily removing NearFutureConstruction and trying to load the ship?

Deleting the ship from your subfolder won't remove it from flight.
You can delete any ship in flight from your Tracking Station already.  Big red button with an X in it on the bottom left when you select the vessel.

The HG-5 is a folding relay antenna, it's just not very strong.
The best way to get multiple sats in one launch is to use the "Interstage Nodes" option on the fairings, which will let you attach multiple stacked payloads without them touching.
(not my pic)

Oh yes.
Although it might be a good idea to plan on getting a discrete GPU down the road, even if it's just a cheaper low-medium end used one.  KSP doesn't need off-CPU graphics, but it does help.