The way I see it my options are:

• Leave the current not-visibly-cracked-but-probably-close cover on and RTV around the edges to try and seal it (costs RTV + possible oil leak/vacuum seal problems)
• Get a 3rd replacement cover and either try again myself or ask my shop to do it ($15-30 + shop labor if they do it)
• buy either a full engine or lower engine off of ebay ($200-$400)
• buy a new bike ($1,000-$3,000)
• go bikeless (I'm leaving the country in less than a year and would probably sell then anyway) (free, but inconvenient)

Can you hold the cover in place with your hand and get a proper fit or does the cover not fit flush to the engine?

If the cover does not flush to the engine case check to make sure that the stator is seated on the crank properly it may be out just enough to keep the cover from seating. ;) :)

No, none of the covers, including the one I originally took off immediately after taking it off, could just be held up to the bike flush, too much weird stuff going on with the magnets, I figured. Getting it off is difficult too. There's no feeling of metal being dragged against anything though. which is why I figured it was a weird magnetic thing.

With all the names (generator, magneto, stator, etc) being applied to different parts in there I'm a bit foggy on which is which. What you're talking about, blaine, is the big metal cylinder that's attached to the body of the bike and rotates around the coil-y flower thing that's attached to the cover? How could it possibly be mis-seated?

Sorry I meant Flywheel.I was just thinking that if it wasn't seated on the crank properly it would keep the cover from seating against the crankcase.Also the magnets make it difficult to remove the cover,that is normal.The coil that attaches to the cover is the stator. ;) :)

Flywheel? Another term? So that's the part that goes around the stator, the part that you're looking at when you open the window to look for the line for TDC?
As soon as finals crunch is over, I'm going to take that cover off and take a close look at the case side of this whole situation. I'll take the stator off the cover and see what I can see about how the holes all line up and all that to try and figure out if the flaw is in the case, all 3 covers (ha!), or just the mechanic.

Yes the part that rotates with the crank. ;) :)

Hahaha, so the good news is, I didn't crack my 3rd, bad news is I did crack my starter driven gear.
http://www.youtube.com/watch?v=8bsC-v4i-og
Any ideas about this?
The shaft coming out of the gears to the left seems to be fitting overly snuggly into its slot in the magneto cover and I don't see the top, smaller gear of that pair on any of the diagrams in the service manual or in the parts fische (though I'm really not sure I'm looking at the right figure in the fische)

you put the small gear on the wrong way

Did you you read through BadBob's tear down and replacement? It had photos and everything. Have I not brought that up before? Maybe it was somewhere else that I mentioned that.