The trans shifter is now only about 1" taller than stock. I would not change it unless it causes a problem. Any time a solid shaft is cut, shortened, and welded back togeather, there is a chance of the weld failing. This is main reason we do not alter the height of the handle.
1980 Toyota - 1997 3RZ-FE 2.7l Engine, Turbo R151F 4.31:1, Triple Turbo Marlin Crawler Billet (2.28x4.70x4.70) = 1,148:1 Crawl Ratio, Marlin Crawler Twin Stick and Short Throw Shift Kits, 30mm H/D Output Shaft, High Angle Drive Lines, 5.29:1, ARBs, High Pinion Front, 25mm HD Billet High Steer Kit, 6 Pin Locking Hub Bodies, 86+ Wide Rear End, V6 3rd member, Chromolly Axles all around, 37" IROKs with Beadlocks, York onboard air - Rollbar air tank, Premier Power Welder, Marlin Crawler 4" USA-made Leaf Springs, Bilstein Shocks, et cetera....