Besides the rear travel, is the frame geometry completely different, or just the placement of the rear shock or the rear linkage?

I just built an 05 Stump Jumper with a Manitou Minute 1 fork (100mm) with 6.5" Fox FoatR hated the low bottom bracket because my pedals kept scrapping roots and rocks. My 99 Stumpy had a BETD linkage which increased the rear travel and raised the bottom bracket to where I rarely scrapped on anything, but since I got an 05 model it was worse than my stock 99 Stumpy.

Has anyone used an aftermarket linkage to get more travel or to raise the bottom bracket on their 05 Stumpy? What is the longest shock I can use on a stock linkage? I know that it would not fit a 7.5" shock without major modifications on the linkage.