Hey Scotty -
Are the cracks small things, almost looking like stress fractures? If so, yes that does happen occasionally but has not proven to be a problem. Check out this thread for more details:
http://www.oople.com/forums/showthread.php?t=11071
The rear bulkhead piece should sit between the rear transmission tabs and the chassis - is that the gap you're talking about? Under the rear tabs only? Once that is in place the transmission should fit well with no spacers. If the front tabs are not fitting down pretty flush, then something else is possibly wrong.
For Lipo, I would strongly recommend NOT grinding down those small braces. Those small sections provide quite a bit of fore-aft stiffness, something which the battery area is lacking. Further, with the LiPo being so light, there doesn't seem to be a disadvantage to running it slightly higher. If you use lead weight to balance the car out, it fits very nicely underneath the battery next to those braces!
~Paul