Ok, first off the 85-86 bottom end won't accept the 87+ cylinders because they are fundamentally different engines.
One has reeds in the case, the other has reeds on the cylinder itself, and that's just scratching the surface of the differences.

As for installing an 87+ engine in an 85-86 frame, it's well within the abilities of an average mechanic.
It's considerably easier than building a hybrid, though the modifications for a hybrid will also allow a 250 engine to be installed with the addition of a 1" spacer.
So if one were to do the hybrid mods to a 250, you could essentially run the 250 indefinitely until you found a great deal on a 500 engine to simply drop in without needing frame modifications.
The most that would be required for a simple 87+ upgrade would be modification of the front engine mounts and downtube.
Replace that single downtube with a 87+ wishbone, or two tubes on either side, would be all that's required, other than carb setup, new pipe, and maybe the CDI.
It's actually very easy work and could be done by pretty much anyone with access to a welder and some way to notch tubing.

There's rarely a situation where you can find "theeeeee best" pipe for a certain engine, as different people like different things.
However, when there's very little competition in the pipe department, sometimes you get a pipe that is so much better than all the other pipes out there that you can declare a clear winner.

For the 85-86, FMF is the best pipe commercially available (ie not a custom pipe).
For an 87+ 250, Matt's is THE pipe to have, not even a custom pipe will get you close without a LOT of R&D.
For the 500's, Jerry Hall makes a great pipe, followed by the Q pipe and AAEN, and Mitch's DCS pipe is starting to look pretty good too.