WELCOME TO THE SITE!!! Looks like you have the right outlook for her restoration. Too often a person will try to do the whole thing in one huge bite and get discouraged when they see how large the job is. Remember, it is possible to eat an entire elephant if you do it in several meals. The same holds true for a restoration... take small bites. Concentrate on one problem at a time, solve it completely and then move on to the next one.
Some thoughts:

The shift shaft used to be a major PITA to repair, but some enterprising engineers came up with a 2 piece fix that makes the job much easier. Look for it online.
Not liking the spun sleeves, nor the alum scuffing on #3. I think a new block or engine is in her future.
Soft decks are most often caused by the wood that's glued to the underside of the deck rotting out. Caused mostly by not properly venting the underside after usage and during storage. Ditto for the stringers. Not really hard to fix, just time consuming.
All foam, including closed cell, will, over time, absorb and become water logged. At 8.34 lbs per gallon it's amazing how many pounds it adds to the total weight of your boat. Check it carefully... Take core samples from several different places, and if it's waterlogged remove or replace it.
Good luck with the restoration and we look forward to seeing more boat porn in the coming months as the job progresses.
Welcome aboard Capt.
__________________
1987 V20 w/1987 150HP Yamaha on a Shoreland'r Trailer
1978 16.5 Airslot w/1996 120HP Force on a Four Winns trailer
1996 V21 w/1993 200HP Mercury on a Shoreline Trailer
All towed by a 5.7L Hemi Durango.
If God didn't have a purpose for us we wouldn't be here, so
Live simply, Love generously, Care deeply, Speak kindly.
(Leave the rest to God)
Silence, in the face of evil, is itself evil. Not to speak is to speak, not to act is to act. God will not hold us guiltless.