I have two soft spots I need to repair and need some help with what specific glass and resin to go with.  Construction is plywood between fiberglass.  Guessing 1/2" plywood, but will confirm when I start to work.

Looking at fiberglass I am not sure cloth, mat, or 1708 which seems to be a combination of those would be the best.  I believe 5:1 resin will work with all of those.

I figure I will make a shallow cut, take off the top layer of glass and clean out the rotted ply.  Cut my new ply and seal it with resin, put it in and put glass over it.

If my methodology is wrong please provide some insight.

When I start in on this I plan to do step by step pictures to document how badly I burger this up.

Sounds like you have it right. Just make sure to layer and step it out. Use resin and mat and make sure to put enough harder in the resin. Use a lot of mat, that's what gives it strength.

Trick I did was to bolt in a piece of aluminum plate under the plywood. Feathered the plywood edge and fiber glassed it in. Counter sunk the bolt heads and glassed over them for a smooth finish. Had to work at it to get the plate under the flooring but once done it was rock solid. Last for 10 years and still holding up great.

Repair was right where everyone stepped down from the back deck. The area took all the abuse.

Also glassed a 4x4 to the hull floor to help support the plywood floor.

I was trying to figure out extra support and a plate and 4x4 sounds pretty solid.

I did the same repair 30 years ago in our old Glassmaster bow rider.  I made the error of using 3/4” plywood. I cut it to shape then glassed the bottom and put it in place, screwed it down and glassed the top.  
Boat was so damned heavy after that it took forever to get up on plane.  
Original floor was 1/4” ply with a thin layer of resin and glass on top.
Keep it thin and light!

I am going to match the oe plywood thickness but know I need a bit more support in that step down area.  I have seen some guys build deck extensions using pink foam board and glassing it.  Thought about trying to build a support out of that.  Also looking at some 1x4 cross members.  I'll ruminate on some ideas before I start cutting.

I appreciate the feedback and will start a thread as I get going.