My '01 Rodeo LS was having similar problems.
The check engine light and Trans light would come on and would either shut down or go into "limp mode".
My mechanic thought it was the EGR, but after I cleaned it and some money later we found out it was my wiring harness.
They temporarily fixed it by zip tying some of the loose wires secure and since then everyhting is fine.
Im getting a new wiring harness put in next week, but the temp fix has held for now.
Check your wiring harness....