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.
Ok so I had a dig around and it sounds like 12 psi is the magic number.
The air is there to assist the spring. Without it the springs aren't strong enough and will bottom out I believe.
samwisemcg's post in 349 Crank Seals was marked as the answer