1997 s10 350 motor swap no spark

[iroc-s-10]

im pretty far into this swap, just a lil bit of history started with a 2.2 pulled and dumped that, bought a 1976 sierra classic pick up with a 350 turbo 400 3 speed. motor ran good and strong, dropped it in the s10 with little mods sat nicely in its new home. so i got it all in and fired. i bought some aftermarket parts edelbrock performer intake, edelbrock 600 cfm barb, and a set of hedman headers, so i took it all down and put it back together when i pulled the cap and rotor from the engine i marked on the fire wall the position of the rotor in the firing sequence and also marked on the bottom and cap as well. when i reasembled it i couldnt line the rotor and firewall together it would just fall into place but about a quarter turn from the original mark on the wall. i could however line up the 2 other marks on the rotor n bottom plate. im thinking that this has been the cause of my problem. when i turn the truck over now it won"t fire, no spark, i noticed while the motor was turning over sparks coming from the alternator as it made a complete turn, the sparks did stop after a few tries and was replaced with a lil smoke.
i guess my question is what do i do now? what do i look for?

i have alot of experience with automotive systems but more with newer vehicles, i dont have much experience with the older equipment but im learning quickly this is my first "hot rod". any help would be gratly appreciated!