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

epoxy thickened with wood flour from your plywood pannels.

: 2. How far behind the backband should the cockpit opening be.

It would help if you told us what kayak are you talking about.

I would suggest positioning the backband on its longest position,
or the longest position you think it will be used in, & then add
3"-4" & that's the position of the back rim.

another idea is to look at kayaks pics to get the correct proportions.

: 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.

dunno. I used the cheapest plywood I could find.

: 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.

An eigth of an inch over the length of the kayak is nothing.
you will not paddle in endless circles.

good luck,

Erez