StahnAileron

Hmm... I personally can't see anything indicative in the output log. Have you checked the ksp_log.txt file as well? It tracks what the game is doing while running. Looking at the end of it should give you a clue as to what was going on when a crash happens. Maybe post that as well. (Though I find it odd you're now crashing on different mods during start-up.) Note: that log can get pretty big though.
If you wind up having to manually check the mods, keep CKAN off and MOVE half the mods out the GameData folder to someplace temporary and start the game. If it starts, exit and swap out the two sets of mods and test again. If it still works, it's probably a mod conflict of some sort. If it crashes in either attempt, you know which half to look at. Repeat the process by halving each subsequent mod set you identify as causing the crash. This should reduce the number of KSP starts and the time you spend looking for the offending mod if it's just a compatibility issue. Mod conflicts will be a bit harder since you need to find the combination of mods fighting one another.
Another option is to start by removing any mods that are plugin-based first (they include or are just a *.dll file; though I'd probably leave Module Manager there for the time being.) However, this COULD cause KSP to hang on loading if any plugins are hard dependencies for another mod. (i.e. A mod assumes the plugin is always available without an explicit check. This will be true with mods that bundle their dependencies or based on their own collection of utilities, like USI or WBI.) This pretty much requires knowing which mods are inter-related. I'd try the previous paragraph first before moving on to a clean install test next, though, unless you know what mods are hard-dependent on others.

Your biggest landing issue is the fact your landing gear is so far from the Center of Mass of the vessel. The wheels at like a pivot/fulcrum when you land. If it's that far away from the CoM, the weight makes the vessel act like a giant lever, slamming the front down. (I'm guessing this is what your hard and bouncy landing probably look like.)
Best thing to do is get the gears just behind the CoM (maybe just a little further than where you have the Center of Lift). Doing this will let the wheels take the brunt of the weight of the craft without torqueing so much on landing. At that point, you just need to adjust the springs and dampeners.
Also, there is no such thing as "too low" a stall speed. The slower you can fly, the more lift the design has to work with. The more lift you can work with, the softer the landing can be.
But yeah, first thing up: move those rear gears forward more. They're way too far back for comfortable landing. In Real Life, most aircraft have their main (weight-bearing) gears near the center of mass for a reason. (The nose-wheel is just for balancing and ground steering, really.) If you have problem with ground clearance (you're hitting the ground with the end of the plane), use bigger/taller gears. (The taller the gears, the further behind the CoM you should place them so they don't wind up ahead of the CoM on ground contact due to your Angle of Attack.)
By the way, moving those rear gears forward will also make it easier to take-off...