Phantom Rotation and thrust forces... is it from clipping?

[Sresk]

Hey all I'm pretty new to the forums and I've recently been running into a bug that causes either phantom torque forces that my sas can't counteract and or phantom thrust that causes my orbits to eventually walk off into deep space. I'm fairly certain that it has to do with part clipping but  I can't pinpoint it.

I'll admit I'm running a ridiculous number of mods 100-120 or so. And I'm not too concerned with pinpointing the issue on any one ship design as I'm ok just scrapping the ship and starting fresh. What I'm asking is what type of design guidelines can I follow to minimize the possibility of running into this bug?

Just to give a little bit of background on the most recent of my run ins with this bug I had an SSTO plane where I had moved the wings very high on the fuselage and just slightly in so that there was no space between the wing base and the body. The plane reached orbit and maneuvered to minmus orbit just fine. But as soon as I opened the bay doors the doors clipped through the wings and immediately I began experiencing some really weird phantom rotation and thrust. I couldn't time accelerate because my craft was under acceleration even though throttle was at 0 and all of my pith was trimmed to 0 (I've read on the problem and alt+x  did nothing to help). I tried jumping to a different satellite in orbit and the orbital view showed that my space planes apoptosis was no longer changing but the bug followed me and would effect any craft that I was piloting. reloading the game to prior to opening the bay doors did not fix the bug but restarting the game and reloading did... until I opened the bay doors. 

I was finally able to restart the game client a third time reload to the VAB slide the wings down to ensure that the bay doors had a clean path to open and everything was fine. I suspected it was a part clipping issue as Id run into the same problem a few launches prior when I accidentally had the edge of an SAS clipped into a fuel tank, again sliding the sas a few inches in the VAB fixed the problem.

So I guess the question is what part are safe to clip and what clipped part have a high likely hood of resulting in the bug?