The difference in intake cam gears, like you mentioned, would likely cause a problem with the UCON. That would be something that would need to be discussed with Gadget. I have pictures of the differences between the two intake cam gears ('03-04 & '05-09), but my bandwidth on photobucket has currently reached its limit, so posting them would do no good right now. :/ I have a '03-04 4Runner 1GR in my Tacoma right now. Had to swap the cam gears.
Next question is, are the ecu plugs the same on your year model as the are with the '05+? If they are, that makes things much simpler, as far as plug n play is concerned.
If for some reason the URD UCON cannot work with it, then you can always use a wire in unit, to tune instead.
Dezod Motorsports Inc-We ARE performance. Scion tC turbo pros! sells AEM standalones. Just look in the Xrunner section. As well as a lot of other engine components for the 1GR.
Everything else is just nuts and bolt then, so if something needs to be slightly modified, it would be easy.
First thing first though, is call and speak to Gadget about his kit.