Coming from someone who's on his 2nd boat redo project, I can tell you this...its a lot of work, but when you're done, you know exactly what you've got from bow to stern.
The stress cracks don't really bother me much with your boat. Its 40 years old...and that would be an odd place for cracks unless your stringers are completely & totally gone, which I'm sure they're not...so most like just hull flex like others have said.
There are tons of restore threads out there to look at. Friscoboater (Jay) has a huge one on iboats, (sorry everyone), that has youtube videos and a million pictures. He did a great job rebuilding his Glastron, and is a great one to look at.
When you do decide to do the transom, I had great experiences with Seacast pourable transom...strong as can be...no wood to rot...
If you're concerned about how far the rot is on your transom, drill a few small holed from the inside! And see if the wood is coming out wet & mushy or dry...that can help tell you how bad it is...make sure you seal the holes with 5200 or another sealer. You can get an idea of what you're dealing with...
Find something that motivates you on the boat...and use it to keep you going.