You've just discovered one of the hardest jobs on your bike.
The easy bit should be the flywheel nut. I found shocking it off worked the best. Get a long ratchet on there and hit the end down with a hammer. The fly wheel will move a little but the compression should hold it fairly still. It may take a few hits before the nut will crack.
The primary gear on my 348 took me months to get off. I went through about 4 different types of gear pullers, some broke and some were too big, so would just slip off.
I eventually bought a puller which worked, it cost about £25 from ebay and looked like this http://i.ebayimg.com/00/s/NTAwWDUwMA==/z/zJ8AAOSwd4tUF4ZU/$_12.JPG.I know some people on here have made their own pullers, which have worked.
Firstly I would say take the clutch basket off so you don't damage it's teeth. If you haven't ever removed this before, do it slowly as there are 3 metal dowels which hold it on the shaft, they may drop out so keep an eye out for them. Get the puller on the primary gear, with a firm hold. Slowly tighten it over the course of a couple of minutes, tighten wait, tighten wait.... Then loosen it off and start again. I did this about 4 times and it eventually popped off while I was waiting. From here it's a simple job to change the seals.
Good luck