Alternator not charging

Actually, it might be....

This is a problem that requires a little background. Three years ago I had a short circuit that burned out my wiring harness from bumper to bumper. Luckily my insurance paid for the installation of a new harness from American Auto Wire. Unfortunately the installer (Ferrari Shop here in Germany) ordered an upgraded harness the required me to buy a new one-wire alternator at my cost, the insurance would not pay for that. Anyway, took them about 6 weeks to get it in. There were a number of little thing when I got the car back like installing the headlights without the adjustment springs, not wiring the lights for the added gauges not in the origiinal cluster....

Anyway everything was more or less ok until about 6-7 weeks ago when the starter drive would not engage the flywheel and my battery was dead. Replaced the battery but the starter would still not engage. Discovered the new Powermaster (3 years old) alternator was not functioning, had the local Bosch shop test it. I also noticed the car had been wired so the positive terminal of the battery was connected as the ground to the engine. I changed the wiring for a negative ground, replaced the alternator with a new one from TuffStuff and got a new starter (PMGR).

Now the car starts immediately but I am not seeing what I expect on the alternator gauge, it rarely reads above 12 and normally is around 11 while driving down the road with about 2000 RPM. If I check at the battery with the engine running it is usually about 12.5. Today I saw 10.5 driving (EQUUS gauge) what could be causing the low charging? Need another ground somewhere?
 
I am not the best at this stuff, but I have heard that Fords, even those back in the days when Ford make good cars (Those were the Days --- ) often developed bad ground wires. In my 99 Mustang six, auto, though mine is a Californian car, so good on rust - my headlights would occasionally flicker very quickly, almost too quick to catch it. And my last alternator only lasted 4 years, and I complained to Ford about that, I was told on their rebuilt alternators that they only use the old shell, that everything inside is new - and it was $800 bucks - I said "so I have to budget 200 dollars a year on an alternator?" - now I wonder if the bad ground shortened the life of the alternator? My mechanic added another ground wire, I don't think you can really have too many. If this Ford alternator doesn't last a long time, some shops still do rebuild your own alternator - I even considered getting into this lost art, though it wouldn't be a wildly profitable endeavor, maybe one could make decent money at it. The parts quality seems to be going downhill at many places.