Eliminate secondary VE, several codes pop up!

[02Ls1]

Well i was having trouble with a 00' model computer that it have the secondary VE. So i decide to elimanting the secondary VE writting a newer file of a 01' file, works fine but several codes pop up.

P0418 - secondary air injection (AIR) Pump Relay COntrol Circuit Bank 1
P1380 - Misfire Detected - Rough Road Data Not Available
P1638 - Generator F Terminal Circuit

My battery light pop up to in the dash board.

This truck have a camshaft i need to tune my VE but i want to know why this codes pop up

[02Ls1]

Can anyone help me out?