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Try to get it easier. Go for a "direct ascent" design instead of doing it "Apollo style". 
You will notice it will be easier to get a good "form factor" for your lander too.
You do not really need legs if you land around 6m/s.
When landing reduce your speed to 90/100 m/s when you are at 10000, then sap all your relative horizontal speed when you are at 500. Just go down straight managing to keep it "brakeable".
About the "general design", maybe you need just a little bit more "oomp" in you transfer stage. 

I did not have a look at the pic but I had the same issue and the guilty part was the undeployed landing gear clipping through two different wings ejecting the wing section on physics start.
I solved my issue attaching the landing gear to a fuselage section.
Good luck.

I made a few more experiments and turns out it was not a wing related issue but it depends on the physics suddenly acting on the undeployed landing gear clipping through two different wings. 
It was ejecting the gears that unluckily where strapped to the outer wings.