So the mounting points on the frame differ from the DTRE/DTR.
Whilst the engine is basically identical, so the actually performance/shape of the pipe won't be affected by the later design, the frame mounting points are different.
It's worth noting, the very early DTR's ran a 3BN cylinder, so there are subtle differences in actual engine specifications. Can you confirm that you're running a 3BN cylinder? Or the revised 3MB cylinder?
I can't remember whether or not the fact the mounting points differ was a deal breaker or not, or in other words, did it cause it to foul the frame.
My gut instinct is no and you should be okay, if you can make a couple of brackets.
I've done something similar with my Aprilia ETX, where I have put a full arrow system off of the SX models. The engine is the same, but I've had to fabricate up some brackets to get it to fit.