Please forgive me i'm terrible at explaining things in text form most of the time, here goes anyways…..

When I tried to take off the Fmf pipe on my 90 lt250r while tearing the head down, I couldn't get it off without lifting the cylinder up a few inches because it was hitting the frame.  My head is now punched out and I got my new piston and rings and I'm ready to put it back together and I want to do some rtv sealant around the exhaust where it meets the flange to help from blowing oil/carbon on the front of the engine.  The only thing is, I would like to fire it up today and not have to wait 24 hours on the rtv sealant.  Is it possible to pull the pipe back off without having to lift the cylinder so I could do the rtv sealant tomorrow or something?

No i didn't unbolt the flange.  Is this the problem?

Yes unbolt the flange and fenders supports braces.

After you unbolt the flange you need to take it off the pipe before you try to take get the pipe out of the frame. The flange on the end pipe will hang it up. Also you might have to take top motor mount off. I think it gets hang up their to.