I also wouldn't be pulling any heads off, not yet.
Toasty mentioned lining up the timing marks, FIRST
Then, if they are off, obviously correct them.
Try to diagnose one problem at a time, or you will wear yourself out fixing e-v-e-r-y-t-h-i-n-g... <img src="/forums/images/graemlins/zombie.gif" alt="" />
Just my 2 cents. <img src="/forums/images/graemlins/rolleyes.gif" alt="" />

98 Gen 2.5
05 Pontiac GTO
91 Corvette ZR-1
2011 Kia Sorento (wifey mobile)
Clarkdale, AZ