Thanks for your reply Jerry. I agree with what you say about the crank needing to drop WAY down. If the crank had dropped "way" down the rear seal installation would have been a heck of a lot easier! I just can't reconcile how my dots don't align.
I think what I'm going to do is pull the plugs and rotate the crank a number of times and see how the timing marks line up (both mine and the ones stamped on the gears). If they never line up, then I'll loosen the bearing caps again and see if the front drops down enough to disengage the teeth. I'll need to do this anyway to get the teeth lined up .
Thanks for the info about the 2:1 difference in the gears. This will help alot I think. Worst case scenario (which doesn't seem so bad) is to do what you say with the soft wire, valves, etc.
Thanks.