Need help to finish my restoration project

I need some assistance please. Narrative appears in regular type, with question and help needed on the bold items.
After a long and painful exercise, my restoration project of a 19' center console outboard boat is close to being finished. It had all kinds of rotting wood problems, transom, stringers, and most recently the deck. I separated the inner liner from the hull and am working on them independently. But, I'm finally almost finished and soon to put it all back together.

I'll group my questions and concerns. I'll edit this and add photos as a thread in progress. I'll post tricks and thoughts I encountered along the way, with sucesses and failures hopefully for the benefit of others.

Refinish Deck/ inner liner:

Replaced the plywood deck core. This is a top view of the area that was flexing: http://www.boatdesign.net/forums/attachments/boat-building/18691d1202497010-advice-needed-deck-repair-boat-deck.jpg Flipped the liner over, cut off the inside skin, and removed all the cockpit deck core, it was about 90% saturated wet and 50% rotten (like wet mulch). Ground clean the approx 1/4" liner skin with a knotted wire cup brush on an angle grinder. Replaced it with a nice exterior 19/32" plywood I found at lowes theat was very clean and clear, and replaced the inner skin with a layer of 1708 biax and epoxy. From a lesson learned by the failure of a guy I paid good money to replace the rotten transom, I predrilled and drove drywall screws to suck the plywood tight to the liner in a bed of thickened epoxy to make sure there would be no air voids between the liner skin and the new epoxy. The drywall screws were removed and I filled the crew holes with pieces of bamboo skewers to keep resin from pouring through the hole before the 1708 skin was lain. When the liner was flipped over, I filled the screw holes from the deck side with thickened epoxy.

I've made a mess of the inner liner, spilled some epoxy, drilled some holes, but still probably only affected 0.5% of the surface area. The existing gelcoat is faded and chalky, with some scratches. The non-skid pattern looks like it was made with a nappy roller (not a diamond pattern or sprinkled on sand) Need help on a finishing strategy. Fill holes with gelcoat putty and roll minor areas / buff-compound out good areas, or paint. There are some filled holes in the deck, mainly in the foredeck from an old bow nav light, the old high rails, etc., largest 1" dia, smallest 1/4" dia., which were filled with some type of poly putty and gelcoated over. The edges of the putty are cracking away from the surrounding fiberglass, and the reflective cracking looks like it needs to be fixed so it won't surface when refinished. Can I grind out the putty and replace with fiber/epoxy? I can use a countersink bit on the smaller holes and dremel a bevel on the 1" hole ??

Deck fasteners.
I need to fasten to the deck, a leaning post, and clips to hold down a poly livewell tank under the leaning post. After the deck replacement, I am ultimately paranoid of any self tapping "lagging" of screws into the deck. Since I need to refinish the deck and I would like to have the leaning post removable, I don't know whether to drill oversized holes and fill with epoxy & fiber, then tap the holes for machine thread screws, or use toggle fasteners. For the toggle fastener holes, is coating the sides of the holes with epoxy enough, or do I need to overdrill/fill/redrill?

On the underside of the deck over the gas tank, I want to zip tie some hoses and conduits. The zip ties have hole for fastening with wood screws. How do you all seal the screw holes? Silicone, 5200, epoxy, etc.?

Hull/Deck Joint:

The joint was made with self-drilling tapping screws with a small bead of white adhesive (came off easily, probably was silicone). The overlap depth is small, about a half to a full inch max. I bought a tube of 5200 for this and a couple hundred new self tapping screws (not self drilling, I will drill pilot holes). Is the 5200 a good material for this?

Tips & Tricks Discovered:

Working with floam floatation. When filling a compartment with 2-part PU foam, make a top form out of a sheet of plywood, covered with plastic sheeting. For example, for a space between two stringers and two bulheads, the plywood spans over all sides. Then when your pour the foam, cover the hole with the plywood, and weight it with your body, concrete blocks, etc. This forces the foam into the shape you want it in and creates a tough skin next to the plastic, and saves you from having to cut off any foam that spews over the boundaries. Before I learned this, I would have to pour a compartment more than one, and wasted time cutting and cleaning between pours. I also used waste foam that I had to cut off, just chuck it into the hole before the next pour, saves money. Do not get the uncured foam on your skin!