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 as a gear flip mod in the trans. I ran normal sized tires on mine. I hate hate hated the big LST/LST2/afterhshock tires. Made the thing handle like a hog. However, there weren't many options for gearing, so I had to spend a bit of money and effort to have a more nimble truck running traxxas 3.8" wheels/tires on it.
I ran it for 3 months with the stock engine and an LST2 pipe and smaller 3.2" zombie maxx tires on it. RPM arms, titanium turnbuckles in the upper arms and later for the front/rear tie rods. It was what I thought very quick off the line and handled really well compared to my revo/savage I had at the time.
Then I put an LRP28S3 in it. Was my first "high end" big block, only surpassed in price a year earlier when I put an OS18TM in my revo.
By the time I got near the "clean running" part of break in with the LRP28, the aftershock two speed locked up on me. Replaced that with the LST1/2/3 two speed.
Shortly after that, I lightened the clutch shoes a bit so it was more snappy off the line:
Then it was obvious the LRP28 needed more gear as it was topping out so fast and wheelies were nearly uncontrollable. I got the RC-Monster +2 pinions with the LST1 threaded bell:
Then I did the gear flip in the transmission which added +1 to the gearing.
It was quick!
However, I started having issues with the 2-speed again. It kept hopping the flat spot and locking up.
I shimmed up the pucks and replaced the hub a couple times but gave up on it and sold it to someone that ended up putting an LRP30X in it.
I did a myriad of other changes to it, but those were most of the ones I recall that dealt with gearing or the engine install. I did run 4 different engines in it. It had a weird flywheel with the back being really cupped/recessed.