Best to have a shop rebuild with the pressed in diodes and you know it will fit. Also get an adjustable voltage regulator as I had a problem with a new solid state vr that would not Allow the alt to work until the voltage went too low.
Always use a battery float minder when car is parked for more than a few days

If you have a bad fuel pump, it could cause alternator problems. The clicking and over heating of the fuel pump relay sound like a problem. You say you did some troubleshooting of the cis system. Did you check total fuel flow at the return line to the tank to see if total fuel flow was up to specifications, 850ml in 30 seconds? If there is some blockage in the fuel lines or filters it could be a problem, is the filter screen in the bottom of the tank clean, system and warm and cold control pressures correct?
You would need an Amprobe to check the electrical draw in the wire to the fuel pump.
Alternator should put out around 13.8v over 1500 rpm. Yours is still low.

Thanks for the input!
@ 47 Silver: Went out last night to check the voltage on the field connection at the VR (blue wire) and it read 14.3V, so I am pretty sure that the alternator is capable of 14.3V, I am also pretty sure I have a good connection on the other side of that wire at the alternator as I cleaned all connections at the alternator before I put it back in this past weekend. Do you know if 14.3V is is in the ballbark? If yes I may move replacing the VR down the priority list, a bit.

@E Sully: I had the fuel tank out a a month ago as I was suspecting crud on the bottom, but it was actually pretty clean. There was old gas in the system since the car was sitting for a year. I thought the distributor was gummed up a bit, but I think things are back in order after new gas and a couple of bottles of various "snake oil" products. Before all of that, I kept adjusting the fuel ratio (with 3mm Allen) and idle mixture (with set screw) as well as idle air bypass to keep it starting and running, but I think I was mostly fighting that the fuel pump cut in an out due to a dying fuel pump relay. Now, with a new fuel pump relay (and some chattering) the relay still gets hot but it allowed me to dial the CIS back in, and she idles and revs better than ever with no hesitation (that I had gotten used to). Based on that, I did not check fuel flow or pressures, only verified the spray pattern on a couple of injectors. I had resolved myself to this being an electrical problem, not a CIS problem. But you make a good point in that they could be connected. Return flow check seems easy enough - thanks for the figures.

I'll probably jack her up this weekend and also check B+ on the starter terminal as other posts have identified this as a potential for a bad connection. Will keep you posted.