I'd give them a call and ask... if it was factory turbo (4g61t), then I don't think they'll give you as many issues... you'll have to de-tint the windows before you take it through, also the steering wheel probably isn't legal either. So long as it has the factory airbox, all the emissions are connected and it isn't all loud exhaust/massive frontmount.. should be ok.
Roof rust shouldn't be an issue as long as it doesn't go through the roof, if it's just on the surface that's fine. Maybe sand it off before you take it to regency and paint it with primer.
They can tell the engine size upgrade by the engine numbers... I'd just call and ask if it's an OK swap and explain all about the car (don't tell them about performance upgrades, just basically explain about the original engine and the swap, what car the swap comes from, and the horsepower rating difference between the two - you don't need to disclose that it's an RS engine, and they won't know, a VR4 2l turbo is 195 horsepower) Is it currently registered with the VR4 engine?
Things like the suspension etc, so long as it's not too low (they will be able to tell you over the phone how low it can be)... I dunno, I don't think you'll have that many issues, it isn't a skyline afterall. Just call them and ask.