Big K, anything below the floor level i would replicate as closely as possible. Im not an engineer or a professional boat builder but i do know that many times things are built in a certain way for a reason, meaning, for impact resistance or strength to a certain area or provides some type of function. I will be changing the floor plan / layout of my boat but will keep anything that looks like it might in the slightest way be structural (everything at floor level and below plus the bow boxes seem to be fabricated in such a way to add strength and integrity to the boat). More specifically, the piece your thinking about leaving out, the drainage cover, i would suggest putting it back how you found it or get an opinion(s) from a real boat builder(s).
If i understand you correctly, your intention is to leave some of that old sea ray resin filler, on the sides no problem, it just has to be sanded to where its not in the way of new construction. i dont think you can leave any on the bottom unless you use the exact same size stringer thickness you removed. If you go anything bigger the stringer will not physically fit, this was another reason i grinded mine out all the way.
I'll bet you a Double Hefty Burger, a large bag of greazy fries and a small diet sprite that that white stuff is cabosil! or a 40 year old derivative there of. Its more than likely their version of PB less the chopped strand fibers.
I grinded my entire hull, but then im funny that way... please let me explain... watch the video below
Usually folks around these parts only use PL when they cant work faster than PB can dry in one layup. Another consideration is PL is wayyyyy less expensive than PB. To circumvent this problem i built my stringers and bulk heads into a frame. The frame sits off the hull and can be removed then put back exactly in the same spot until i was ready to PB it to the hull a quart at a time. I dropped the PB in on one side of the stringer, pushed it through making sure i had complete fillage and coverage of every millimeter under the stringer, then once i was sure it was packed i made the fillet on the far side (the side where most of the PB was pushed to), then later came back for the opposite side fillet. Sometimes you can do the fillets on both sides of the stringer simultaneously but you want to be very cautious not to disturb the filling already under the stringer by moving the PB while forming the fillets.
Theres nothing to figure out when drilling transom plate / gymbal housing holes, the template is already there for you on the outside, you just drill from the outside in. However, it may be a good idea to put a piece of wax paper up against your keyhole from the inside so that you can get a tracing of where you have to drill at a slant in for your steering. (There will be a certain degree of slant for your boat). Some of the drill holders that u you use to make the perpendicular holes also adjust for slants.
When your sanding please wear protection and get a fan blowing if possible, then sand with your back to the fan or from the side. If you think that the neighbors are planning to put a hit out on you for causing dust storms, have somebody hold a shop vac where you're sanding or tarp off the area. HF has really nice pop up canopies for 69 bucks, they are well made and you cant beat the price. I have two. Its a pain in the but cheeks to keep taking your cover on and off, also, once you finish your deconstruction its not a good idea to let the sun hit your hull continuously, plus if you had the canopy your top would be covered then you'd just have to drape a tarp around the sides for sanding sessions, this would keep the dust down and make your neighbors love you again!!! HA HA
If theres anything i can do to help please let me know, and if you need to, PM me and we can exchange numbers and emails, i may be able to stop you from making some of the mistakes that i made and learned from the hard way.