One thing to keep in mind is that different steps of a full set-up can affect the prior steps. So some level of re-iteration is usually needed. Your intonation seems way off on the E (I think you said the high E, but perhaps not) and the A strings.
In general, a good order for doing things is to:
1. Put the new strings on (if changing strings), and do a preliminary tuning first (as the string type and gauge can effect step 2)
2. Make sure the neck relief is right (truss rod adjustment if needed)
3. If the truss rod was adjusted, let it sit for at least several hours, and perhaps a whole day, then retune, etc.
4. THEN set the action (raising or lowering bridge saddles, or bridge end-points if you don't have individual saddles). Doing this will throw the tuning off, so re-tune after every adjustment. Make sure you are happy with the action feel, and don't have excessive fret buzz, etc.
5. THEN, check the intonation. Move the saddles backward or forward to correct, assuming that individual adjustments for each string are possible. In some cases all you can do is adjust the bridge end-points. Retune after every adjustment.
Doing things in a different order may require going back to re-do prior steps.
I didn't mention anything to do with trem height, level, range, etc., but making sure the basic height and levelness are OK should be done early on in the process, and then you can fine-tune the trem levelness (and the "range of pitch change") via adjustments to the trem claw screws at the end, since any prior changes to the bridge and/or saddles (action or intonation) may have a modest impact on the trem.
The PRS web site (in the customer support area) has decent descriptions of what to do, recommended settings/specs, etc.
One other comment on intonation is that it depends highly on how hard you tend to fret notes. So what's right for one player isn't necessarily right for everyone. And it is also highly dependent on action height, so if someone makes an action adjustment after doing the intonation, it will be off afterwards. And of course string brand and guage has a big effect on intonation, so if there's been a change in brand and/or gauge, the intonation may be off. If you tend to break high-E strings a lot, and then buy single-strings as replacements, this can throw things off a bit, after the change. I have one guitar that doesn't have individual string saddles (you can move the bridge as a unit, including angling it, but that's it), and it could be set up OK with either a set of 10's, or with a set of 9's. Since I used to break .009 E-strings a lot, I tried using a set of 9's, but with a .010 high-E string swapped in. There was no way to intonate things right, with the single-piece bridge.
