Tested each of the test points and got mostly good voltages, there is a 36vac test point that produced only 18vac on the regulator/audio board along with an unregulated 10.3vdc point that was cranking out 11.5v, a -22 & +22 vdc that were both at 23v and finally a +5vdc high up on the auxillliary board near the right upper corner that had only 4.75v. I also discovered r29 on the regulator/audio board is fried, probably recently as I now no longer have any video just the spot killer.
I don't have a board in front of me, but the 36VAC should only measure that across the two sides of that AC line. Transformer is center-tapped, and the CT is grounded, so each leg of the AC will only measure about half of that voltage relative to GND. There should be two TPs for 36VAC; one connected to J9p4, another tp J9p5. Have to measure AC across these two to expect the full 36.
Unregulated "10.3" at 11.4 doesn't sound like a big deal. Hey... it's unregulated

I think it's actually an INPUT to the A/R board, not an output. It's used to generate the regulated 5V, and power the audio amp. It's rectified in the power "brick," and filtered by the Big Blue" capacitor. Which reminds me; if your Big Blue appears original, you might check the AC content on the 10.3 unreg line. I forget how much is generally considered "OK", but replacements of those caps are widely performed.
The +/-22VDC are used by PCB video output amps, as well as the audio amps on the aux board. I just realized that the "3rd printing" on arcarc.xmission.com is missing sheet #3; get those from the 2nd printing... they include the aux board. Anyhow, these voltages are good...
4.75 is at the low edge of the specs for 74LS ICs. Power comes to the aux board via a few pins in the edge connector. Check/replace the pins in the housing, and check/clean the PCB edge traces.
Regarding the fried R29... This is a symptom of the +5V "sense" circuit either "going bad" or "doing its job." There has been a long-running Holy War regarding this matter. There are two camps: those who say "that's the way it was designed to work; it's an indication that there are bad connections between the AR board and the PCB, and they should be fixed." and those who say "that's suipid, I'm just going to do the sense-mod and be done with it." Personally, I don't perform the so-called "sense-mod" on my Ataris. (But I do not wish to re-ignite a flame war on the topic). Do some googling with the terms atari, R29, sense mod, etc. and you'll find plenty to read. In any case, if your R29 burned, you had a lot of current flowing, so you should check (again) the molex power connectors on the AR board (both ends) and the edge connectors at the PCBs (both ends) for burns. What this tells me, is that at least one of the pins (in the sense line) wasn't making good contact, and that you might consider rebuilding your edge connectors. A good crimping tool isn't very expensive, and the crimp-on terminals are cheap too. I buy things like that from Ed at Great Plains Electronics:
http://www.greatplainselectronics.com/Category-35.asp ,
http://www.greatplainselectronics.com/Category-53.asp Bob Roberts also sells this sort of thing, as well as "kits" of parts for fixing/rebuilding the AR boards:
http://www.therealbobroberts.net/ar2.jpg