[jons7e]

What I should expect from a shop for initial tune/set up of a new set up? The shop I purchased from is new to me. When I asked about this while ordering the guy said, “We can go as far as you want…”
(I am thinking peep and my sight axes set and a paper tune, is that normal and customary?)

They will setup nock sets, d loop, peep, rest, verify timing, you will shoot the arrow you intend to use with the bow (which is important in tuning) through paper (insist on you doing that with your release), ... that's about all you're getting.

Here's where it actually gets interesting (because all of the before mentioned is a few screws, tied knots, and burning ends) and what separates a good shop from one that turns and burns or doesn't know better, ...
If it's a near bullet hole, moving the rest a few clicks is OK.
If it's nock high or low, moving the rest up or down is also fine.
If it's a large tear left or right you should use top hats, period, and some shops will get lazy and not change them and instead just move your rest, and that's not acceptable. If they attempt to do that, I'd tell them to not bother and leave with the bow untuned but everything attached to the bow ready to go. Go back later when you're use to shooting the bow, or find another shop if this happens. Besides, you need to retune the bow after everything breaks in (string/cables) and you get use to shooting it, and that's the tune you actually care about.

BTW, you're just basically tuned at that point. Then to truly tune the bow, you need to get field points and broad heads hitting together, and that's typically small rest movement stuff. If you use mechanicals, you still need to do this step. If you never plan on using broad heads, then you can use am unfletched arrow. Be forewarned, when you remove fletching, you are see all of your form issues in the flight and it can confuse you when tuning, so this is for consistent shooters.

Is there tuning that should take place before stabilizing set up is installed to not disguise form issues then fine tune with the stabilizers are installed? Or does that just make extra work?

I would attempt to tune the bow without anything else on it other than the before mentioned basic setup. Then as you add a sight and quiver you can balance with bars. You want to use the minimum weight needed to achieve the effect you want, and most bows are pretty well balanced and vibration free to begin with.