Unfortunately, the measurements do not exactly match the existing
door. The used door is 1 1/2" shorter

I would add a scab to the bottom edge, then put a brass kick plate on
both sides. No one will notice if you don't point it out.

From context, I presume that by "scab" you mean an extension to the
door. I question if this could be made to look good. If not, it's
not really a suitable option. While I'm not a carpenter, I expect
that I can find someone who could modify the frame to fit the door and
make it look good, expecially since the frame will be painted.

Also, there
are two 2" holes drilled in it. The deadbolt hole is not even close
to where my existing deadbolt is located and it's too big.

Visit a good locksmith. He'll sell you a deadbolt that will use your
old key and fit a 2" hole. Move the strike plate on the jamb to match
the new deadbolt location. Fill and paint the old strike plate
location.

Thanks. I'll check this out.

Can a hole be filled in such a way that would not be very noticable
with a clear coat finish?

Short answer: No
Longer answer: You can either make it obvious*, disguise it, or cover
it up. If you patch it, it will always be detectable.

* First rule of decorating: If you can't make it match, make it stand
out.

I hadn't considered this but it could work. If I can't find an
internal deadbolt that fits, I may go this route. After all, it IS a
recycled door and that's part of its charm. Perhaps NOT trying to
hide the old hole has merit.