I know for a fact the wireing wont fit, but im pretty sure the engine will slot straight in, just check the mounts and where it all bolts in, should be able to compare by sight
Both engines have electric start, do you know what wiring bits I would need to change? Also, will I be able to use parts from my old 2006 DTR engine in the new TDR engine?
i've never actually looked at a tdr loom before, but I know pre 2003 DT's don't fit DT's over 03 models, alotta cuttin an crimpin needed to be done (not exactly sure what tho), but i am sure about the CDI connection and ignition, you'll need to figgure out how to mod the cdi plug on and switch the ignitions over, and as for the parts, I don't see why you cant use them, they're identical engines, so you'd probably get away with shoving all your 06 bike parts into the TDR, or vise versa.
There isn't a lot of wiring with the engine, just the small ammount coming from the left hand casing. You wont be touching anything complicated wiring wise as you'll just be using the existing DT gear. If the plugs for what wiring is there are not the same it'll be straight forward enough swapping the electrical parts over from the DT to the TDR engine as mentioned above.
The only mechanical defference i can think of is the TDR engine will have the old type old oil pump and your DT will have the new type. I'm note sure if there's any advantage using one over the other though.