I thought you were going for that E-Locker, if you're not taking the locked rear then you won't have to worry about the gear ratios. The Auto Trans was simply geared differently at output shaft than the manual hence why Toyota put 4.30's in the Auto's and 4.10's in the manuals, if you are just plugging in the trans I'd keep the 4.30's they should give you a tiny bump in low end power. (I'm about to be putting in a 4.30 E-locked rear out of a Auto and will have to change my front diff (clam-shell) to match the rear ratio if you don't have matching ratio's front and rear you can have NASTY transfer case killing bind.)
The 3rd members ARE swappable but not without modification to an open Diff rear axle, and that still leaves the question of the front diff. Search for E-locker retrofit. It involves removing some studs and drilling and tapping holes for new studs as well has cutting a reasonable notch out of the axle housing where the e locker mates up. I didn't want to bother with that and will be jumping to 33's once I get my lift so the lower gear, however slight, is also welcome, it just means I'm going to have to replace my clam-shell up front as well and that's a ***** from what I hear...