4wd lights flashing

Played in some mud in 98 f150 5.4 and truck was stuck in 4wd lo. Removed 4wd actuator from transfer case and manually switched to 2wd high. Now truck doesn't like to downshift during normal driving and truck hesitates during acceleration. I've read this is something that happens and this truck is known for leaking windshield causing problems with the GEM. Wanting more info and is the GEM responsible for the unusual shifting or what all can be causing this? Please help!!