: 1. Is there a putty or something that can be used hide the wire tie holes on
: my hull panels.
that's a lot of work for little gain IMHO, I mean you'll spend a lot of time with a squeegee but just as likely to smear staining epoxy putty,,but if you want to do it then as mentioned thickening with various thickeners along with sawdust powders might give a good match.
: 2. How far behind the backband should the cockpit opening be.
that's kind of variable depending on the boat, you and the cockpit, how about 2-6"?
: 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.
The weight is minimal, if find the 3" bulkhead can be used to store lights and flares with holes cut into it.
: 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. Will the boat paddle in circles or something.

nope