OK - it sounds like maybe yours is stuck as badly as both of mine were. The idea is to use several pushing/pulling forces instead of one big one, and heat, heat, HEAT! to expand the cylinder aluminum around the dowels and loosen their grip. The base gasket joint really doesn't have much adhesive force compared to the rusted dowels, but it's important to loosen it too so the cylinder comes off straight.
This is my flywheel puller - I use it sitting on a wood block on the case top, with another small wood piece between the bolt head and the underside of the cylinder's intake opening:
http://www.amazon.com/K-N-82-0150-Pulle ... B000FGCYN0This thing can apply plenty of upward force against the cylinder, with little risk as long as it's pushing up against the main cylinder casting and not a fin. If possible, you can slide it towards the side that has the dowels (on the MR motor this is the left side, I think it's the same on the MT).
This is my 2-jaw puller - I hook the jaws on the cylinder top's two shortest/strongest fins available, pushing down on a wood block or plastic drawer pull on the piston crown at BDC. NOTE: only a LIMITED AMOUNT OF FORCE should be applied to the cylinder with this puller, otherwise you could snap a fin. I've used this successfuly a number of times now, with no problems at all (don't forget the heat !!).
http://www.ultimategarage.com/shop/imag ... 04-400.jpgOnce the two pullers are in place and tightened up, use a heat gun to apply heat evenly all around the cylinder/case joint. I've got an infrared thermometer, and have applied well over 300F to this joint with no issues. Keep applying heat - especially on the dowel side - and occasionally tightenng the pullers (especially the intake-side one) and eventually you'll hear and/or see the cylinder pop loose a bit, possibly with a bunch of rusty penetrant pouring out as well. You can also whack the cylinder with a rubber mallet all round to speed things up, but keep an eye on the pullers as sometimes they move around from the mallet blows.
I'd be very careful how much force you apply to your lifting handles. The cylinder threads are just M6 in aluminum, and can deform easily. It would suck to end up with leaking intake / exhaust manifolds.
Ray