I think my previous post was a bit harsh, which isn't constructive.
Let's start all over, since Wheelie has provided us with such great pics.
The SR500, TT500 and XT500 motors are essentially the same. The 600's are the same, only larger, with two exhaust pipes and two carbs. None of these engines carry any oil to speak of in their crank cases. The oil is pumped into a storage tank via the hoses seen looped in RisingSun's pics.
If you look carefully at Wheelie's pics you'll notice that the top frame tube also serves as an oil tank. IIRC it holds 3 quarts and is about 3 1/2" in diameter. The TW's backbone is about 1 1/2" diameter and 15" long. It holds 486 cc's, or about half a quart.
So you'd need an oil tank. Which would pretty much eliminate any chance of an air box or a room for a battery. A 3 quart oil remote tank would have to be roughly 6" in diameter and take up most of the available space for these things. Or you could re-engineer the top tube of a TW frame to look like the SR frame, which is longer, so you'd need to up the TW top tube to 4-5" diameter to get the same capacity, then try to find a gas tank to fit over it, and so on.
Oh, by the way, the 500 is long enough fore-and-aft that your front tire will now hit it. That'll need some creativity. You've also lost about 2" of ground clearance because your front sprocket has to maintain the same geometry relative to the swingarm as your original motor, but your 500 has a deeper crank case. Speaking of sprockets, which end do you want to have a custom sprocket made for? A 428 for the front, or a 520 for the rear? How's it goin', so far?
A TW motor weighs 75 pounds, 4 oz. ready-to-run. Care to hazard a guess what a longer, wider, taller 500 weighs with all its plumbing, oil tank and 3 quarts of oil?
Those are just a few of the engineering issues involved. I'm quite confident that once all the height, width, offset, exhaust, carb clearance and other unseen issues were overcome and you began addressing the real world issues such as braking and suspension you'd quickly realize that your new toy outweighed an XT500 and was zero fun to ride.(Don't axe me how I know this
The path to Nirvana has had a fork or two)
I have examples of almost every Yamaha thumper ever made sitting either in a bike or under or my bench. Trust me, if any of them were suitable candidates one of them would be in a TW by now.
If you wanna play with a project that has a reasonable chance for success I'd recomend the XT/SR 250 or 350 motors. Both have been done, both involve major surgery and compromises, but either stands a better chance of being rideable within the TW platform.
Or pop a light weight, compact. air-cooled, old school big bore 2 smoker in there, shove it all the way to the left and go out and kill sumpin'.