Sounds like you have it all under control... Do you have the factory manuals?
I was just about to post you the manuals link, but flicked back to the photo of your drive, and the year you posted... I see a discrepancy... You posted that it is a 1988, which is an Alpha One, but the photo of the lower unit shows an o-ring on the top of the drive shaft... and a squared off anti-cav plate... This would indicate that the lower is an 'R' (1983-1984), not an Alpha One.
The manual link is the same ->
https://docs.google.com/open?id=0B1TAvwZ3TjhfOVRUNEk0anBUR3lQYTkwcUh5RElUQQ
What's your engine? I'll post up a link to that too...
Chris.........
Found it... 1988 3.0l, replaced in 2009.. Was that a full 'drop in' engine, or a long block using your old 'add-ons'?