You'll have to make sure your motor mounts are modified or changed to accommodate the wider engine, keeping the clutches in line. Also I would consider whether the cooling system on the 400 will be sufficient to cool that big engine.
You're looking at a lot of engine mod, full swap over of everything but the drive train and I would still want to be sure everything drivetrain is up to the challenge of running with the MUCH more powerful engine.
That makes more sense. Any triple is going to be similar work. You're dealing with different exhausts, air box, mounts, starter, throttle cables and choke would have to come with it, same with any electrical - ignition, stator, mag, etc. It doesn't mean it can't be done, the bodies are likely similar but again, almost all engine parts likely won't be directly interchangeable.
580 XLT Triples and a 650 Indy Triple, 2 completely different engines.
Yes straight piping it would hurt the engine. You would be better off with stock only. The Indy 400 Chassis had a 600 Available to it, the 600 was the same pistons as the 400. In '91 they went to a 650.
Straight pipes will also make you lose HP, as the pipe is "tuned" to the engine. The restriction in the far end of the pipe is a certain size and distance from the exhaust port. When the fuel ignites, it has a pressure wave that leaves the exhaust pipe and expands to the restriction, then rebounds back to the cylinder just as the fuel/air mix is being drawn into the exhaust. The rebound shoves the fuel/air mix back into the cylinder where it can burn and make power. Without that fuel that got shoved back into the cylinder, your air/fuel mix will be lean and a lean air/fuel mix can burn hot enough to melt your piston.