I'm making my first part with my mill and it's a pretty diverse part. It has everything including contouring, deep pockets, drilling, chamfering and tapping. I think it's a good way to learn how to use the machine and CAM software.

So far, I did one side of the part. I did the steps progressively so I wouldn't be taking cuts that are too aggressive. I also drilled the bores to 1/2" first to allow chips to fall out and left .005" all around for a nice finishing pass. The depth of the pocket is 1.3" so I set my tools only as long as they needed to be. Still the flutes were not that long and you can see some lines where the mill shank was rubbing.

Based on this picture, does that surface finish look decent? Can I get it better? I took off the last .005 climb milling with a 1/4" 3fl end mill at .25 DOC, 3200rpm, 20ipm. I cannot actually feel any ridges, but I can see the little ripples.
Attachment 201174

Anyway here's my question:
Now I need to flip the part over to do the rest of it, which is basically facing off the top, finishing a couple holes, chamfering, etc. What is the best way in general to do this? As you can see, I have stock that prevents me from indicating the part itself. Am I supposed to indicate the corner of the vise and then push the part into the corner? What about indicating the Z height?

My concern is that this has to be absolutely perfect or else the contouring I do will not match with the existing curves and there will be a ledge. Any pro tips for doing this? Seems like it's such a common thing that no one bothers explaining it.

Thanks!!