Having never done exactly what you are doing, I can only tell you what I'd do in a similar situation. TDC 1 on the old motor, TDC 1 on the new motor and swap the flex plate over in exactly the same way it came off. It may be pointless, the flex plates are only supposed to go on there one way, but if you start from the initial setup, things are less likely to be off. At the same time I'd swap over the distributor and align number "1" on that also. Probably wouldn't be a bad idea to remove the old CPS and mark the center between the bolt holes on the old flex plate, it may be too late for you to do this though.
A few basic measurements from the get go and if things don't work out for you, you have less to check. I've read many threads about guys who had issues after swapping motors. And have gone nuts trying to figure out why it doesn't work. I may be wrong, initial setup may be more important than just swapping over the flex plate or it may not, I'm not the sharpest needle in the sewing kit, so I tend to stick with the basic steps I learned in school. I'd treat it just like a new rebuild, less the cam timing. Then if something does go wrong, you know for sure it isn't the initial setup.
If you already have the motor mostly bolted up, it may be easier to unhook the tranny and transfer and slide it back to replace the flex plate. Just be careful to keep the torque converter seated all the way in. The last time I swapped out the same year (actually one year off but same series) engine I gave the torque converter one last shove and twist and it seated another 1/2 inch deeper and made a satisfying thump. I often wondered what the outcome would have been if I hadn't gotten lucky and after reading about the guys who fired up their new motor and the tranny didn't do squat, I tend to think seating the torque converter is important. I loctite all the bolts on the flex plate and torque converter bolts. I use new torque converter to flex plate bolts if available (a holdover from my Dodge days, they always recommended new bolts here) and I use a torque wrench for these.
If you forget to hook up the firewall to engine head ground, things are also doubtful to work out well for you. A lot of guys have forgotten this ground.
