tony stark

the timing chain in my 1993 pickup broke. i replaced the chain, spockets, guides, tensioner & water pump while i had it apart.
this is when the problems started. upon completion the motor would run, but it shook so bad i thought that it was going to hop out of the truck. i did a compression test and on #'s 1 & 4 i got little to no compression. i blew compressed ait into the spark plug holes on the dead cylinders and got air out of the intake manifold ( i did put each cylinders at their respective tdc comp. stroke ) . #'s 1 & 4 intake valves were bent. i lapped in 2 new valves, did another compression test and now it starts and idles and revs just great. problem is a intermittant back fire ( a true backfire, up throught to the air box ) and no power during acceleration.
i have checked the timing 5 degrees btdc w/ connector shorted, the erg the pair, sorted through and rechecked all the vacuum hoses checked for vacuum leaks.
i am beginning to think that when i had the head off the timing got messed up. there are 2 bright links on this (toyota factory part) chain that lined up with the sprockets on the cam & crankshafts, does anyone know if these marks are evenly spaced? when i put my motor to tdc compression stroke on #1 the bright link is lined up with the timing mark, does that mean that the bright link is lined up with the timing mark on the bottom of the crank sprocket. am i one tooth off or do i have yet another problem. i don't mind pulling it apart AGAIN but if that's what it takes, fine, just don't want to to it AGAIN and still have the same problem.
sorry for the long post, just figured more information was better than to little