I've got a line on a 2000 grand am with the 3.4 that runs good for $500.
My 2003 grand am engine is junk, a replacement with short warranty from junk yard is $550 but guaranteed to fit.
I'm thinking after swapping the engine I can junk the 2000 and only be into it for couple hundred bucks.
But I'm worried about getting it in and finding some small change that is a huge hassle.

Anyone have experience with this?

what do you mean its guaranteed to fit? if they have year cross references that say its the same then you shouldnt have an issue.

Is there such a cross reference?
I've just heard people who had problems using different year engines and finding the wire harness different or emissions issues that turn in to huge headaches.

i imagine they might. if they both have the same engine rpo, same car and vin engine letter, they are likely the same. most they would change might be different sensors that would have to be swapped from your engine to the junk yard engine