1) What I found just testing with the Cruiser Bridge in the neck (along with the Fender single coil in the middle), a listening test to my ears showed the standard DiMarzio humbucker wiring (white+black connected, red=hot, green+bare to ground) sounds the best alone (switch pos. 5) and when combined with the single-coil middle p/u (switch pos 4). Does this sound correct?
Yes, I believe series connection is the default standard for these pickups (as for most).
2) I am next going to install a Cruiser Neck in the middle pos, and the AT-1 in the bridge. For the AT-1 if I use the same switch wiring as is already there, I believe switch pos 1 is going to use the AT-1 both coils in series, switch pos 2 is going to use one of the AT-1 coils (split) in combination with the middle (Cruiser Neck) pickup. Will this be acceptable as I believe the Andy Timmons configuration for switch pos 2 has the AT-1 coils in series, and in combination with the Cruiser Bridge (middle pos.) p/u. Can anyone comment on this? I don't fully understand (yet) the switching and how to make it like the Timmons configuration (rather than the Fender configuration).
That is correct. Pos. 1 is humbucker in series, pos. 2 is humbucker split + middle pickup. I have no idea how AT's guitars are set up but if you want the humbucker in series also in pos. 2, you can just disconnect the black/white wires from the pickup from the switch but leave them soldered together and put some isolation tape around them. Try both and see what you prefer.
3. On the pots, check with a multimeter what value you have (you need to disconnect the switch before doing that, otherwise you will get the parallel value of pickup DC resistance and pot DC resistance). In general humbuckers are used with 500k log, and single coils with 250k log but that is just a rule of thumb. With a fairly powerful humbucker such as the AT-1 I would go with a 500k log volume pot and add a 470k resistor in parallel for the single coil positions so that they see a load of close to 250k.
4) With only the neck p/u replaced (Fender Single replaced with Cruiser Bridge), the Fender Single coil in the middle by comparison is slightly louder and with lots more treble. Does this sound normal? I believe it will balance out once I put the other Cruiser (middle pos.) and AT-1 (bridge) in.
I don't know the stock pickups in your guitar so it's difficult to say whether this is normal or incorrect. But with all the pickups replaced at least the Cruisers should be in balance with each other. The AT-1 will have quite a bit more output. Many players like a higher output bridge humbucker in HSS, others want a humbucker that is closer in output to the single coils. It's personal preference.
Cheers Stephan