Of considerable importance to me would be making sure the base under the skin is fully supportive of the skin. Looking at the 2nd picture it appears that the RHS is flush with the bottom of the skin whilst the LHS has a considerable gap. Is the difference perhaps stuck to the bottom of the old skin?
I would use side rails and a router with a wide surface cutter
to cut the existing plywood to a good level, equally deep over the whole area and if possible able to accomodate a standard thickness of ply to come level with the bottom of the existing floor skin. Quality of ply? Phenol-bonded pine ply. Inexpensive and will last for 50 years. I would use one sheet, not a series of squares.
You mention that the skin is full of cracks. Stress cracks? Structural cracks? Because for me 1st prize would be cleaning
off the ply on the underside and refitting it. Firstly it would be the correct thickness, secondly it would have the non-skid finish that youíve been used to. If it remains usable for a repair, I would use it. Getting a decent finish on a newly laid GRP floor is not easy.
The existing ply needs to be dry or no adhesive
will hold. I second the use of epoxy. Acrylic
resin is not well-known for sticking to old acrylic
resin. Epoxy sticks very well and is not as expensive as one would believe. Use West System 105 resin with 206 (slow) hardener.
Laminate the new ply to the old, using a layer of thin chopped mat between the new and old ply and on top of the new ply, paint
the bottom of the skin with wet epoxy and laminate to the ply. Use a series of weights to place even pressure over the whole area - something like a number of clay bricks. I would do this whole laminating job in one session.
When itís all set, use some epoxy with fairing thickener (micro-balloons) to fill in the seam around the edges. Fair the seam off to original levels.
Finish of with two-part epoxy paint - it has a great finish, is very hard-wearing and easy to apply with a brush or small roller. Iíve used International Perfection Topcoat with good success. If the old floor just has stress (spider web) cracks, this paint will fill them.
You will no doubt get a number of suggestions/processes from others. Look at all of them then choose what falls inside your self-perceived skill set. This is not as hard as it appears.