I am currently doing battle trying to install the mid exhaust section on an 04 Sy 250.I have 2 new rubber seals in the mid section.

I have cleaned the header pipe with sand paper and greased both exhausts and still it refuses to go on.

Any tips.

I am guessing its the one that came off it and its not slightly crushed....You tried a successful fit-up minus Orings first?...not uncommon for substituted wrong seal thickness as Oni suggested

Success by polishing the header pipe,reaming some off the rubber o-ring with a die grinder, and using various pieces of timber and a rubber mallet.

There is no leak from the header and the old mid box I welded.

i'd suggest the new rings you've used are a tad to thick. The mid box should slide on lovely with a smear of grease without the use of any encouraging impliments.         On a side note, the ally mid box is easily punctured/damaged where it touches  the sharp corner of the raised boss on the crankcase where the engine numbers are stamped,  Dressing the sharp corner with a file or dremel  is a wise move if it hasn't already been done by a previous owner. HTH.

HI if I take my Exhaust off do I need to replace the O rings or can I reuse? 

Losen a bit front pipe to cylinder bolts.

Resurrecting this dead thread as I just faced this exact dilemma and for anyone else who comes across this issue. 

in 04 there were two part numbers for the o-ring dependent on frame number. I found I was trying to fit the wrong o-ring for my bike number. So if you have 04 bike double check!