Check for  power drain. Test light between ground point in trunk and neg post. Should be zero/light don't burn.. Close the doors and disconnect clock/radio. IF you show a drain..start pulling fuses until the test light goes out. Then you have isolated the "system" that is draining the battery.
6s6 

Is this how it's wired (based on your description)?  If so, think about wiring directly from the megafuse either to the solenoid or to the battery.  You need the most direct route possible (fewest mechanical/electrical connections) from the alternator output to the battery. 

do you have the right length belt? if its too long, it will be too loose, making it squeal, and not putting out enough.

do you have the right size pulley on alternator? incorrect size pulley will not turn alternator fast enough at lower rpms.

do you have another alternator to try?

can you move the battery to the front of the car closer to the alternator and see if you have an improvement? maybe the length of wire is too long from front of car to back.

Thanks for the responses.  I'll try to answer each of the follow-up questions.
50vert
- Alternator Light - No I have the stock guage.  My car was originally a sprint 200.  Guage is connected to power junction block under the hood, since solenoid is in the trunk.
- I did run the green / red from the alternator plug directly to the key Red / Green wire, bypassing the pink wire resister.  Assumed I needed full 12v like the modern coil does.  Does the Alternator need less than 12.3 volts to trigger charging?  Key on Engine off, I read 12.3v at the alternator connector for the Green / Red wire.
sal - Not sure by what you mean by check for drain by touching negative to ground.  When I do so w/ my voltmeter set to 20 dc, I show 0.  Resistance ohms also shows 0.
John - Your drawing is pretty much correct, though the connection at the fuse panel has both wires connecting, rather than a passthrough.  See linked drawing showing all my connections.  I don't have enough 4g wire to test a direct connection from power lug to solenoid, but I can buy some more and try it, possibly tomorrow.
MachTJ - I believe Mega fuse is good, since when car is off, I show 12.6 volts @ alternator, which has to pass through fuse to get to alternator.  Can the fuse be bad and still allow low amperage to get through?  When I checked voltage, it was at the power post, mega fuse, and alternator post.
Markin
- Belt Size - Well, I got a belt that fits best I can tell.  I had to try a few, before I found one small enough, since I'm not running A/C currently or smog.  I aligned the belt and tensioner the way I found on the internet.  See attached pic.
- Alternator pulley is the pulley that came on the '94 3G alternator.  Believe it is the same as the normal '88 mustang, howerever I didn't measure it.
- I do not have another alternator.
- Moving would be difficult, since starter wire is already run through the door channel and successfully hidden.
wsinsle - I ran a wire from trunk negative post to my volt meter, then touched the alternator case and showed 0v.  When I touch the high power lug on the alternator, it show 12.6, since the alternator is wired to the mega fuse which connects to the power lug.  I do not have a direct ground wire to the alternator.  I relied on the case. Is that a problem?

I labeled my drawing to show where I was checking the power in my original post.  A, B, C, D, E





 

Good to know that it needs a resistor.  Clearly I missed that in all the reading I did planning this setup. I'll try to locate one and wire it in to see if it makes a difference.

I really don't think the resister is necessary, it's just there to keep the path if the light bulb burns out (if you use a bulb). I don't remember using one on mine, but I guess it's still worth a try. Some other things I would try, check the connection on the white/black wire to the stator is good and tight. Check the voltage output of the alternator form the out put terminal to the case of the alternator. One last thing, disconnect the battery after starting, then check the output voltage. (Not with EFI) In your case with EFI, I would probably try another battery.

Alternator is definitely not putting out any power at all.  Checking voltage on the charge post is the exact same voltage as checking at the mega fuse or power lug.
Stator is connected to the White / black wire.  It is on the drawing, though it is kinda small.
Unfortunately, resister did nothing for me.  Basically it dropped the voltage almost an immeasurable amount of .01.
Pulley's are probably my issue.  These were the pulleys on the donor, so I didn't investigate them any further.  Crank pulley appears to be underdrive, because it is 4.5".  Stock is 6" I believe.  Alternator pulley is 2.75" and is the one that came on the 3G.  WP is amount 5 3/8.

Currently I don't have smog, PS, or A/C, though I intend to add A/C, so I stuck with a CCW water pump and when I looked into getting a dummy pulley, I could have sworn I saw my current belt layout, though I can't seem to locate it now.
Maybe I just need to get a dummy pulley for the A/C and either a bigger crank pulley or smaller alternator pulley so the ratio is correct.
I do not have a ground wire on the case of the Alternator. If I check voltage by touching the Alt case with my black probe, it shows the same as everywhere else.  Does it need a ground wire or does grounding through the mount and engine block suffice?

soonerfan wrote:

Alternator is definitely not putting out any power at all.  Checking voltage on the charge post is the exact same voltage as checking at the mega fuse or power lug.
Stator is connected to the White / black wire.  It is on the drawing, though it is kinda small.
Unfortunately, resister did nothing for me.  Basically it dropped the voltage almost an immeasurable amount of .01.
Pulley's are probably my issue.  These were the pulleys on the donor, so I didn't investigate them any further.  Crank pulley appears to be underdrive, because it is 4.5".  Stock is 6" I believe.  Alternator pulley is 2.75" and is the one that came on the 3G.  WP is amount 5 3/8.

Currently I don't have smog, PS, or A/C, though I intend to add A/C, so I stuck with a CCW water pump and when I looked into getting a dummy pulley, I could have sworn I saw my current belt layout, though I can't seem to locate it now.
Maybe I just need to get a dummy pulley for the A/C and either a bigger crank pulley or smaller alternator pulley so the ratio is correct.
I do not have a ground wire on the case of the Alternator. If I check voltage by touching the Alt case with my black probe, it shows the same as everywhere else.  Does it need a ground wire or does grounding through the mount and engine block suffice?

I would start by getting the correct stock size crank pulley. If your current pullies are a set of underdrive pullies, its possible that the wp pulley is actually larger than stock.  So you might want to get a stock wp pulley as well. The tensioner should be next to the alternator where those holes are.  You need to grind away about a triangle worth of metal to get alternator to fit right on that bracket once the tensioner is in the proper place. And get the proper length belt.  A belt that's too long won't let the tensioner tighten up enough. I don't think there is any need for a ac dummy pulley. The stock altenator was not good at charging at idle, add to it an underdrive pulley, and you really won't get any output from it.

I do not think you have a pulley miss-match issue, but try brining the engine RPM up to 3000, or so, and check the voltages.  If you're still not getting charging voltage, it is not the pulleys (unless it is not spinning at all).
I agree w/winsle, check all the wiring connections on the alternator for resistance.  You can also try using a straightened paperclip to get into the alternator connections to check voltages, but be careful not to ground the clip.
Although I do not think it matters, verify the alternator rotation is the same as tested at O'Reily's. 

All I can say is if younz was a steeler fan, you wouldn't have issues. I'm running out of ideas of things to check. I still feel there is a small possibility of battery issue. Seen them do strange things, my be worth swapping with another. Another thing you could try is disconnect the main wire from the alt to the mega fuse and measure voltage at the back of the alternator with the car running. It the voltage is up over 13 volts, maybe the alternator can not produce output under load. Did the place that tested the alt just check for output voltage or do they check the alt. under load. With everything else checking out, it is really looking like a bad alternator.

Figured out the issue.  Turned out to be a pulley / serpentine belt problem.
Since O'Reilly had told me the alt was good, I decided to spin it on my own w/ my air wrench to see if I got power.  In doing so, I noticed that I was getting about .15 extra volts, which was nice to see.  I hooked it all back up and noticed I was not getting .15, but was getting about .05 volts, so I decided it must be a belt or underdrive crank pulley issue since I didn't have a traditional belt configuration.
I bought an idler pulley and mounted it on the AC delete bracket, then reinstalled the bracket and like magic I have 14.6v now.
Thanks for the suggestions guys.
 

Funny how people think they can spin the alternator for free...like with elect. fans.  This pretty much prove that there ain't no free lunches.

BB