Thanks for the congrats!
As to setting mesh I lean to the little bit tighter mesh than a sloppy one. I've got friends that set a bit looser than me but I've not had any problems. I find that being on the loose side with the mesh makes the drive train a bit louder and I'm sure it causes more wear and tear (I haven't been able to prove it, but I believe that). I try my best to use something with a 90* edge like a clear plastic protractor when I align my engine so that it looks like its aligned properly looking from the top. When I believe everything is aligned I then tighten the engine bolts to almost tight but some slippage allowed. I then put my finger on the CB and rotate the spur gear to make sure that I have the same play/mesh thru out a full spur gear rotation. This sometimes cannot be perfect because either the spur or CB could be a bit out of round. Just make sure everything is close and go from there. Then I suck the engine bolts down tight and recheck the spur/CB to make sure nothing has changed or binding.
As to bearings I use rubber shielded from my LHS. I do want to try some Avid bearings tho. Can't go wrong for a $1.00 apiece.
I just re-read my first comment and I meant to say to check the alignment holes that are drilled in the chassis that they are straight. If not, even the engine mounts will be out of line. If possible try to find another Prospec chassis to lay on top of yours and check to see they (holes) are the same. Things can happen to make your chassis out of line just a bit but not really noticable, even from the factory.
I can also tell you that I race on rough tracks with big air jumps. I've been told that I need the Z brace for my truggy but like I say its stock and I've had no problems with chassis flex. And I've had some really bad cartwheel landings or landed completely upside down first after 35' of air after attempting a quad about 30' in length.
I shuddered everytime but was able to drive away as nothing happened. Obviously, that is a testament to the Jammin CRT Pro but I sure don't like that happening. But that has proven to me at least that if the chassis is braced well the cars are tough. I have no doubt that the Mugen vehicles, especially the Prospecs are tough as hell as much as my Jammin is. So that takes the flex problem out of the equation.
I have used the vented bells and I really like them. You can check your shoes without taking the CB off because of good visibility to the shoes to see if they need any maintanence. The Vented CB's also help to disipate heat to because of the less rotating mass.
Try these ideas out, I'm sure you'll find the problem.