I'm preparing to put down glue down bamboo flooring on a concrete slab
and have a couple questions. I've already tested the concrete for
humidity and PH and it is o.k. The slab is way above grade.

Hmm, not sure if a vapor barrier is needed. Make sure to look at the
manufacurer's recommendations. Wood directly on concrete is generally
not good.

1. I removed the carpet tack strips from the perimeter and the little
nails broke away some of the concrete when I removed most of them. How
should I fill these holes. Do I use the same self leveling stuff as I
am going to use the fix the uneven spots?

The self leveler will work fine. Just make sure the concrete is clean
and free of dust before applying it. Make sure you vacuum the concrete
well before starting the install.

2. The floor itself has alot of remnants of the drywall and stucco
process. Just alot of white on the floor. There is also overspray
around the perimeter from the painters. How clean does the floor
actually have to be?

A hand scraper is all you need. There are ones that have extension
poles so you don't have to kneel. Just scrape off whatever you can. As
long as there are no ridges you'll be fine.

The transition between the wood and ceramic is a bit off, how much
of a slant can the t-moldings take?
Can't help you on this one. My guess is if it looks good and feels
stable then it's OK.