Ok, so I found where the missing bolt goes, it did fasten a lower sheet metal piece:
So I buttoned things up and installed the new Interstate battery. I tested the voltage on the battery at 12.4V.
I then fired her up, first crank. The little cigarette lighter volt meter was showing 12.1-12.2V. I pulled out the volt meter and measure 14.5 volts at the terminal in the engine compartment, the red wire to the right of the blue fuse. The wire below it is switched and measured 12.2V
I then measured the battery while the car was running at 12.2V. With the car off, the battery is 12.4V.
So I still have some sort of charging issue. So let me quickly recap what's been going on the last 3 weeks when this started:
4th of July weekend we pulled the engine to replace a transmission seal
7th of July I drove 400 miles to Rochester, NY all fine
8th of July I drove 400 mile back to MA and that's when the charging issue started showing up and I started the other thread to get some diagnostic help. My battery was very old so I decided to replace that. My alt seemed to be having a problem so I decided to replace that too. The 83 alt has the built in voltage regulator so in essence I replaced the battery, alt and VR. Today I got it back together and am still having the issue. Any recommendations?