: 1. Is there a putty or something that can be used hide the wire tie holes on
: my hull panels.

Someone suggest epoxy mix in with wheat flour. You can add wood sanding dust to darken the color. Epoxy / wood dust mixture appears darker than epoxy coating the same wood. Test a small amount to get the wood / wheat flour ratio right to get the correct color match.
But you'll have to sand that flat before glassing. That is too much work for nothing. I did mine just rolling the glass over (holes and gaps) and let the epoxy sip in to seal the hull.

: 3. Has anyone used 2" minicell for bulkheads. The 3" seems really
: thick and heavy. I was thinking about slicing alittle off for other parts
: of the boat.

3" really don't weight that much more than 2", but get 50% more glueing area. I think that is more important.

: 4. The hull panels are slightly unfair running along the chines of my boat.
: Also the panel joins at the bow and stern mismatch by about an eighth of
: an inch. Like a dummy I glued it all together already.....
: Is this not uncommon.

My boat is also slightly crooked, doesn't have any problem goes where I wanted.

Will the boat paddle in circles or something.

Only if you want to.