Given you are starting out on the fun of messing around with bits of boat..........
TWO questions you should ask at the outset (of any job):
1) has the cause stopped?
2) is it structural?
For no.1 I am guessing the PO either fixed the leaking windows long ago - or you will be doing so! and for No.2 that your fix won't be structural (obviously important that it have rigidity into the sides - but nonetheless even if you "fixed" the problem with a tin of white paint
?!) the keel
won't be falling off!).
In which case I would also treat it as an ideal way to get hands on with fibreglassing / Epoxy! Really not that hard to use, reading up and patience goes a long way - what makes these jobs ideal is that the results will not be structural and
will be hidden from view so neatness of finish not a consideration!
So whilst the previous ideas have much merit me would be tempted to get the angle grinder out (or the Dremel!) to cut the fibreglass away and have a damned good looksee (and poke with a screwdriver).....if the plywood is rubbish chop out as far as needed (in depth
and width and either scarf in a piece of plywood (saves on epoxy - $$). Scarf does not have to be neat (or even that close!) as will then use Epoxy filler to fix in place..........to finish off then simply need to lay on some layers of fibreglass / Epoxy (read up on how to do that and prepare the surrounding edges).....being out of sight means the patch does not have to be invisible / flush (although good practice to try doing that) and also IMO a good idea to start to learn how to use a disc sander gently (really shifts dried epoxy).......and if you want the results hidden then add a coat of white paint
(I use bilge
paint - including on the ceiling!). WHite paint likes hiding sins!
For those windows, what you may want to consider during replacement is fixing the edges (when the frames are removed), if open plywood at the hole edges then no surprise that water has crept along......my fix would be to scrape / drill out a 1/4 inch of even the good plywood and replace with Epoxy filler so that even if (when?!) a window frame does leak again that it "only" comes inside! Better than new!
LATE EDIT: Just re-read the OP, not sure whether window removal
is going to be happening anyway - if the PO fixed the problem and windows don't actually leak anymore I would monitor
- and for that I would make sure the headlining could be easily dropped (in fixings = screws and in size of panels), likely find that useful anyway (cable runs / deck fittings).....and have a looksee every couple of years. or so