As I replied to your e-mail:
Sometimes there are different length hardware used at the factory. I try to supply bolts that work with *most* of the 3rd gens, but every once in a while they don't fit. If the old bolts work, fine, if the new ones work with some washers, fine. If you want to return the unused bolts with a list of the desired lengths, I can send those to you.
Did you check the t-case shift lever for binding?
http://www.4crawler.com/4x4/ForSale/...l#ManualTranny
Regarding the shifter location, if it is angled other than vertical, it'll appear to move in the direction the lever is angled. That is if the lever sits angled to the rear and you raise the body, the lever will appear to move back since as the body raises around it, the intersection of the angled lever and the plane of the floor of the body moves back. If you want to re-center the lever in the opening, you can bend the shifter back to a more vertical orientation. Another option is a short throw shift kit:
http://www.4crawler.com/4x4/ForSale/...l#Installation
This both raises the shifter 1" and also cuts the angle that the lever sits at (by half) and that combination restores the lever to about the stock location with 1/2 the old throw.