The 140/90 rear tire may have clearance problems if you have the stock saddle bag supports. The sidewall can rub against the bolts that mount the supports on the inside of the fender. Performance wise the tire is a little taller than stock and will reduce engine RPM's about 2%-3%. Different manufacturers have slightly different profiles,  Hope this helps.

Well, rubbing doesn't seem to be a problem, as I don't currently have any saddlebags or supports on there, currently . It is a 90 that is on there from the previous owner. Dunlop 491s are what are on the bike, at the moment.

I have noticed that the extra height does interfere with my ability to get a socket up there to undo the side rail bolts on the inside. At least, I'm guessing that's my problem seeing as others have been able to get to them with their tire still on .

That's what I was planning the next chance I got The wrench part, anyway.

Use a box wrench - not a socket.
Ratcheting box wrenches are even better - they get into lots of places so you can do what you started without needing to take apart things that are not broken.