Rick that seems to be the route most take? Trying to get a feel if that is the best option.
Then you'll need to decide the deck (floor, sole) height. If your transom is open and your engine weight low, you'll only need to raise the deck height an inch or thereabouts. So you can leave the former deck edges in and re-floor on top. If you do this you can leave the liner wall sides intact and tie-in there. The downside to this method is you're building on top of an edge which is cored with plywood 40+ years old
I will be closing the transom and using a porta bracket with a 150 Yam 2 stroke. And as you mention I am not keen on joining to 2 inches of 40 year old ply, sealed or not. I do want finished gunnels. So I was thinking of leaving the bottom skin of the floor all the way out to the middle of the stringer. Then removing the wet foam if it is wet. Then reinforcing the skin and laying glass all the way to the other stringer. Then use a thicker core to get some height and finishing the floor on top of that. This way I would keep the integrity of the liner.