I have my 3800 and Getrag on the cradle (88') but being my first time I need help with getting it set correctly, so what do I need to line up etc...

What are you using for mounts? I'm assuming for the Getrag, you used your existing ones, do you have a mount solution for the engine? Are you building your own?
As long as the axles go to the same spot as stock, and the engine is level and straight on the cradle, that's it. Good to go. There is plenty of room around the 3800 in the fiero bay (with the exception of the alternator, requires notching the decklid in its stock location).

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Build thread for my 88 + 3800NA swap

For a manual, I just try to make sure it is level looking. Your stock transmission mounts are going to be your mounting guide, the motor is just along for the ride.

I am using a fieroflyer engine bracket, rodney poly engine mount, and the poly tranny mounts that were on the donor swap... the only difference is the swap is now on an 88' cradle where before it was on an 86'

Doggy