I think you guys are stressing over the whole rta thing, I know that qld transport are much stricter, but it wouldn't vary much..
As for cutting your frame - adding a loop to the rear will pass without engineering. This is because the part you are cutting off is not structural, you are not changing any dimension by adding the loop.
They are not so much strict on cutting things off the bike.
The rear seat cowl if extended far enough to the rear will also act as a mudguard, as long as it goes the the furthest part of the rear wheel.
The front Guard is a bit of a tricky situation, it has to cover the area of tyre from 12-3 o'clock or vertically up and directly east from the axel, however your frame will technically cover from around 2ish-3, this will all come down to who does your inspection so you should take the time to go down (don't call) and talk to them so your on the same page... It's also sometimes a good idea to get your mechanic to do some work on the bike e.g my mechanic will be doing my final wiring (mostly because I hate wiring, but also because it makes them feel like they know the bike.
My mechanic also told me as a rule of thumb, obviously apart from the frame loop, make everything possible a bolt on piece, that way it's easy to remove or change if needed.
All in all it's all gonna come down to who you get to do the inspection, if they are a relaxed mechanic who is into bikes, they will let alot of it go, just make it all neat and make sure the loop is welded neatly and looks to be almost one peice like it was factory, chances are they won't even bother lifting the seat off to see it anyway...
Hope this helps (I started to ramble a bit in there, if you wanna chat about it any further feel free to PM me
Cheers
Ryanh