It sounds like you're on your way to a good job on that bottom. If you have not gone through the gelcoat, you're probably in good shape with a Chris Craft. I agree their gelcoat is about as good as any yacht ever built. If you think you need protection at the patching areas, you can use a barrier coat either spot coated or on the entire hull, but I have never used one and I have had good results.
Two names come to mind: Pettit and Interlux. THey are both to be considered top of the line. You can't go wrong with either one.
Here are a couple links to Interlux information
http://www.boatersland.com/barrier.html
http://www.boatersland.com/intbottom.html
I have used both Interlux and Pettit, and they both make great products. The Interlux Yacht Enamel is about as good as it gets for upper cabin use and wood boat hulls. Pettit, on the on the other hand, makes that Copper Bronze I like.
http://www.reddenmarine.com/site/new-detail.cfm?id=PET19331
Pettit manufacturers directions for fiberglass are as follows (for the Copper Bronze):
All Bare Fiberglass, regardless of age, should be thouroughly cleaned several times with Pettit 95 Fiberglass Dewaxer or 120 Brushing Thinner. Good luck doing that in the Oakland, CA area, they may send the VOC police after you. Sand thoroughly with 80 grit sandpaper to a dull frosty finish and rewash the sanded surface with 95 Fiberglass Dewaxer or 120 Brushing Thinner to remove sanding residue. Then apply two coats of Copper Bronze, following application instructions. Careful observation of the above instructions will help ensure long term adhesion of this and subsequent years antifouling paint.”
Hope this gives you some ideas to think about.
Tom