Runner,
Never heard of anyone developing a tool to remove the transfer case oil fill plug. Some pipes fit so close in that it would be problematic to get that plug out without removing the pipe anyway.
Not that hard to remove the pipe. Every one (brand and model) is different, though. Basically, you just remove all the mounting hardware for the rear of the pipe(s). Just leave one bolt still barely attached.
Then remove the two header, flange nuts (8mm
hex). Then the final nut from the tail section.
Sometimes the flange is troublesome coming off, but after the nuts are all off, you hold the pipe in both hands (header and tail), and work the flange off. Be sure you protect the rear (lower) pipe with clean rags drapped over the tail section.
To get the pipe back on, you should strongly consider replacing the copper crush washer that goes between the header and the engine's exhaust port. You can get them from auto parts stores for about 1/3 the price of the Yamaha ones. Here's the part#:
AutoZone part#: Fel-Pro 23588, (less than $1.50ea last time I looked)
Put all nuts/bolts back on loosely before tightening anything. Then tighten everything a little at a time.
Moderately tighten the header nuts. Too much torque and the flange on most aftermarket pipes will bend.
Then ride for a few days, and then check the flange nuts tightness again.
That's about it.
Hope this helps.