2003 Jeep Wrangler Limp Mode (42RLE)

When I clear the codes it does go into first for a few seconds then instantly set either the p0720 or the p0731
 
I think wiring is still the first thing to check. You should note number one in the service manual for P0731 does say low fluid can cause this so be sure that ain't an issue. Especially if you just purged. Codes only mean something when your fluid level is correct.