Haines hunter rebuild questions

Hi just starting this thread as I am currently undergoing a rebuild on my haines v17r
The boat has been gutted before, by me 2 years ago and sent to a fibreglass shop to get stringers done new floor and side pockets etc.
I am now in the process of replacing 2 gussets up the front that join the dash+hull side to the floor I also want to extend the side pockets up to these.
I am also going to extend the main deck about 800mm up the front as i want to change the lay out a bit now.
I also intend to replace or repair the transom, I am going to drill a few sample holes In the inner skin to check its condition. But would like to hear what you have to say on this subject

But for now I have a couple of quick qustions

1. I'm taking back the flow coat throughout the hole interior of the boat which was put on by the fibreglassers, my reasons for doing this are, me and my brother are not happy with the finishing job they have done and we want to change the coulor to a darker one. He is a painter so it should be an easy job for him
I want to know after it has been keyed up and nearly been taken back to glass, should I put a later of resin over it then re paint or clean the keyed up flow coat with acetone then paint straight over?

2. I am looking at either fixing or replacing the transom, it is still solid as a rock but the top inch has become soggy due to water pertrusion through an unsealed top cap this is only on either side of where the motor mounts as it had a transom extension about 5 years ago so the centre portion has been sealed properly.
Do I dig out the soggy top on either side and bog it then re glass the transom skin to the top deck or replace the hole transom? Now if I replace the hole transom I assume it have to remove the outer skin as it's a near new stringer setup and floor and I don't really want to cut that out, if I do this method after the transom has been replaced do I re laminate the old outer skin onto the new ply or bite the bullet and relay the hole transom skin and glass into say a 3inch tab I leave around the perimiter?