not that i've done a conversion or anything, but i imagine that the parts (assuming they're from a GC8) should fit in directly. wiring will probably be a mess. you also will probably have to get creative with the steering rack location as well. the exhaust will obviously have to be completely reworked.
legal issues-none that i know of as long as it passes all the regular checks.
smog-good luck.
certification-assuming it passes emmissions and all that, i doubt very much that the tech is going to notice that its a JDM engine. besides, its not illegal to modify your car as long as it still meets all the saftey/emmissions crap.
repairs-well, obviously the warrenty is gone. also, if you damage something in the JDM parts, thats where the replacements will have to come from. replacements which you will have to order yourself more than likely. if this car is your only one, if something breaks you could be seriously hosed.
all that being said, there are a few other issues you might want to keep in mind. J-spec performance engines are designed to run on 100 octane gas (which they have at the pumps). the best you can get at most places in this country is 91-93. this means that your going to have to change the fuel/timing maps more than likely if you want to run standard US pump gas. i know here in st louis, the gas station across the street from the big oval carries 99 or something like that, but its ~$5/gallon. another issue is if you want to rally it, there are certain safety rules that you must comply with at the very least, such as a roll cage, underbody protection, a fuel cell (unless you gaurd the gas tank really well), driving suit/helmet, fire system, kill switch, etc. rally cars just don't make very good street cars
anyway, i'm in no means trying to discourage you, just pointing out some things to help you make the right choice. good luck!