This is interesting... Your track bar didn't hit at all? All TJs are different. Mine hits hard enough that it's not a simple grind for clearance. I'd have to get the cutting wheel out. However... My shocks don't come anywhere near hitting the lower spring perch... Which I know some guys have trouble with. Might be the shocks (Bilstein 5100's).I don't have a rear track bar anymore, so I can't help much there.
I know the gas tank cross member can be trimmed to clear the bracket. Even with a relocation bracket, mine wasn't an issue when I had it. Stock arms, body lift and 1" of rear bump stop all factored into that. My rear was bump stopped for the shocks.
2003 Rubicon