Foxster

1. Make it smaller or
2. Make it in parts, launch them, assemble in orbit. You know, like they really do
3. Use the cheat menu to set it into orbit

Generally, if you radially attach something then it has the full drag of the part. If you attach it in-line to a similar-sized part then the drag is reduced - and it makes no difference if you then translate it away with the offset tool - as long as don't rotate it. 

The craft looks stable regarding fuel. The dry CoM is actually forward of the wet. 
First guess: the airbrakes are forward of the CoL and close to the CoM. That might cause some stability problems when deployed. 
I'll have a fly and see what happens...
I think it's draggy at the front. That blunt front end, the RCS, ladder, canards and Divertless Supersonic Intake are all adding to the drag at the front end. 
You will also find it flies better if you move the tailfin back, plus turn off roll and pitch on it. Similarly on the canards and flaps if you turn off yaw.  
Questions: 
What is the Whiplash for? 
Why so many intakes?
Update:
Yup, I'd say it was too draggy at the front. I tweaked a few things to streamline it, plus a few more bits and pieces, and it flies fine now...

Craft file: https://www.dropbox.com/s/owm2lxjf3mqrdkg/LaythePlaneMk1 Fox 2.craft?dl=0
 

Does your lander have a free node at the bottom? If not then try making the part you want to attach the root part - you can do this even if its placed off the craft and so greyed. 

You don't need a big craft...you need an efficient craft. 
Three things to consider in achieving this:
You should get the payload you are returning to orbit to the absolute minimum. That means dumping absolutely everything you don't need to make orbit before lifting off: chutes, airbrakes, landing gear, experiments, struts, etc. Don't be tempted to throw on extra crew, unneeded solar panels, RCS, reaction wheels, batteries and such.
You need the best engines for isp and low drag to suit Eve. This will likely mean Vectors and/or Aerospikes for the first stages and a Terrier for the final stage. 
For Eve the biggest challenge is drag, so you want to keep it skinny! You want a small number of thin mk1 stacks. You also want to eliminate absolutely anything that sticks out and is otherwise not essential. 
A final thought on your craft design for Eve: If you get the urge to add something to gain just a little more dV then you are likely wrong - you need a "what else can I take away" attitude instead.  
As for landing on land...There are some very large land masses in the equatorial region. Do a couple of orbits and you should spot one. Set your Pe so that the orbit end is to the eastern edge of the land and you will almost certainly land in an area to the west of that.  
 

You have a few common Eve craft design problems going on there.
The answer to a failing Eve craft is almost never to add stuff - it's about taking stuff away. That and reducing drag - that's more important than messing with almost anything else. 
You can greatly reduce the accomodation mass by using a mk1 capsule and a mk1 crew cabin instead of the mk1-3. 
Get rid of the RCS completely - total waste of payload.
Dump all the 'chutes, airbrakes and anything else to do with landing before leaving Eve.
You seem to have a probe core in there half way up. What's that for?
Get rid of the struts (very draggy and heavy) and use auto-struts. 
Go mk1 all the way to reduce drag. 
What's in the service bay? 
Dump the solar panels and anything else bolted to the outside of the craft. 
 TT-70 Radial Decouplers are very draggy. Use hardpoints instead. 
Make sure the stacks are pointy. 
Vector engines are the best lower stage engines on Eve. A Terrier for the upper stage is good. 
What are those black and white striped things below the RCS tank?
Once the mass (and drag) are reduced a lot you won't need the RCS and additional reaction wheels but you will need some kind of fins at the bottom. 
By having a heatshield in there I'm guessing you plan to bring the lander back to Kerbin. If so, don't. Do it Apollo style. Just get your three crew down to Eve and back to Eve orbit, nothing else at all. Have the mothership do the rendezvous. 

Physically they are about 12Mm from each other. Emotionally they are worlds apart. 

Yes. Supposedly gonna be fixed 1.4.3. 

I think all of those mods are available via CKAN, which will install and update the mods for you. 
 

The ratio O to LF is 1.2:1. 

I based my comments on flying your craft on Duna. 
You want about 1750-1800 dV to make Duna orbit, depending on how efficient your lift is and the starting altitude. 
A launch TWR of about 1.3-2.0 should work OK. 
I did see you have a kind-of hidden stage in there. Using it meant dumping the science experiments so I wasn't sure if it was supposed to be used to reach orbit. It did have a problem in that the small tanks were too close to the engine and they became stuck to the engine, preventing proper separation of the spent stage. 

The problem is that the heatshield is super draggy and the back end is hardly at all. So the craft flips to fix this instability when you get into thicker atmosphere. 
The fix is to make a lot of drag at the rear of the craft. 
RCS or reaction wheels will not cut it. 
Try putting maybe 8 to 16 air brakes on decouplers (so you can dump them on the surface) attached to the rear of the craft. Make absolutely sure that when they are deployed they are within the occlusion shadow cylinder from the circumpherence of the heatshield or they will almost instantly burn up. 
The mission as it stands is very likely a bust. 

It's a bit like the wobbling you get when you build a large base. It's been buggy for a long time, no real fix for it. 
Your best bet is to have just one claw holding a single small-part-count craft. 

Rather than hacking the config file, the more elegant (and reliable) method is to use Module Manager to make the change.
Create a file called <anything you like>. cfg  in your GameData folder containing this text ...
@PART[*]:HAS[@MODULE[ModuleCommand]]:Final { %MODULE[MechJebCore] { MechJebLocalSettings { MechJebModuleCustomWindowEditor { unlockTechs = start } MechJebModuleSmartASS { unlockTechs = start } MechJebModuleManeuverPlanner { unlockTechs = start } MechJebModuleNodeEditor { unlockTechs = start } MechJebModuleTranslatron { unlockTechs = start } MechJebModuleWarpHelper { unlockTechs = start } MechJebModuleAttitudeAdjustment { unlockTechs = start } MechJebModuleThrustWindow { unlockTechs = start } MechJebModuleRCSBalancerWindow { unlockTechs = start } MechJebModuleRoverWindow { unlockTechs = start } MechJebModuleAscentGuidance { unlockTechs = start } MechJebModuleLandingGuidance { unlockTechs = start } MechJebModuleSpaceplaneGuidance { unlockTechs = start } MechJebModuleDockingGuidance { unlockTechs = start } MechJebModuleRendezvousAutopilotWindow { unlockTechs = start } MechJebModuleRendezvousGuidance { unlockTechs = start } } } } Assuming you do have the module manager mod (get it if you don't) then this should make all the MJ functions available from the start. 

The more mass the craft has the harder it is to slow it down. I'd try leaving off all the junk and maybe trying something like I posted above.
The first has plenty of dV and a high TWR. So you can deploy the air brakes then burn retrograde to set the Pe to about 20km and then leave firing the engine again until about 250m or so to slow down to <8m/s by the time you meet the dirt.