Bill--
1. Avoid the G10. It's very expensive, heavy, unnecessary, and will eat every edged tool you use on it (I am not exaggerating. You WILL need new saw blades). Patch the bulkhead with plywood closely matching what you have. Cut the rot/bad area out and make the new piece fit mechanically as well as you can. Treat all affected areas & edges with WEST epoxy, and when it dries check your fit again. When it's ready to go, duct-tape it in place on one side and, using epoxy with a bit of filler (just enough to keep it from being runny) and a putty knife, trowel up the edges and the gap. Work it in completely. When it's dry take off the duct tape and do the other side too. Sand fair when dry. This should be perfectly adequate.
After that you can decide to 'glass the bulkhead to the cabintop; but the 5200 method I mentioned will serve quite well.
Also-- consider using Durawhite to paint the bulkhead-- very traditional, bright and cheery, easy, and pretty. It bonds very well to otherwise-untreated epoxy. I've used it all over my boat.
2. I had not observed that your CPs were THAT much out of symmetrical. That looks like about 4 inches' difference. That's absurd. (BTW my point was that the boat was well designed. I never said Hunter Alachua was known for quality control!) If you have the opportunity I would remedy that. Just do yourself a favor and measure both sides. from the side face of the mast outboard to the shroud attachment pins, first. You might find a very odd surprise there.
Even if the boat is a little asymmetrical (mine is too), you can mitigate this difference by cheating a little each way. Maybe just choose one side to move. Mark the athwartships line of the bulkhead on the deck and removed the SS plates. Duct-tape the holes from the bottom and fill from above using glass fibers and epoxy. Then chop out a new hole using spade bitts, a saber saw and a Dremel, and reinstall the CPs where they belong better. (This is exactly how I fixed First Light, a 1977 C44, a few years ago when we replaced corroded SS chainplates.) Remember, don't obsess about a little inaccuracy-- any improvement to what you had is an improvement.
BTW, there is a lot of discussion about this, but I think I would tend to attach the CPs to your newly-epoxied bulkhead with 5200. These two substances, 5200 and epoxy, go very well together (in fact when one is applied while the other is still uncured they expedite the curing time of each other). 5200 is very good in a shear load, which is what CPs bolted to a bulkhead are in. The epoxy saturating the plywood is a very good surface for 5200 to bond to. Just sand a little and wash with mineral spirits or acetone first.
Whatever you do, replace ALL the attaching fasteners with new, preferably of 316, not 18-8, SS.
Also, avoid silicone to seal the CPs in the deck... unless you would like the deck to leak and soon rot the core and the bulkhead. This is also another good application for 5200. It's strong, flexible and able to keep out water. Just consider-- if this job is done right, how old will you be when you have to chip out the 5200 and fix that bulkhead again when it rots next time? (With silicone I predict it'll be about in 3 to 5 years. With 5200 I predict about 25-30. Do the math.)