here is a link to the EPA's regulations on engine switching (engine swaps)
I found it interesting
http://www.epa.gov/compliance/resour.../engswitch.pdf
From what im seeing, you can modify your car, remove equipment, move things, ect, as long as the car still passes the tail-pipe test. So long tubes and relocated cats are technically ok.
As for engines, you can swap a newer engine into a older chassis, but not an older engine into a newer chassis. Its legal if you retain all the systems and emissions controls as the original setup.
And as a side note to bills post, if you have collectors status, dont miss your instpection date! You will lose you status and have to re-apply, which is a much harder thing to do now than it used to be.