The alignment of the pinions (LST uses 2 on the bell) and spurs is pretty tightly dictated as your not really able to move the engine at all to compensate. It's one of those trucks that would probably benefit from a slide type engine mount like you would find on 1/8th buggies/truggies. Probably...
No problem. I used a spacer like that on my first bell so I could run 3 bearings vs just two.
http://www.beatyourtruck.com/forum/showthread.php?53261-How-To-Triple-Clutch-Bearing-Mod-LST&s=c97252a2c2691c6ed2bd6373e8b7bab4&p=653630&viewfull=1#post653630
Can you post a clear close up photo or two of your problems? I can't picture what your trying to get across.
I had an aftershock back in the day, which was a LST1 more or less, but they ran the same flywheel. I ran an LRP28S3 in mine with +2 gears on the bell over stock from rc-monster as well...