1996 Honda Passport Electrical/Alternator

I have a 96 Honda Passport 4x4. I took it to a local shop to get it inspected the other day and when they hooked the computer up to it they noticed my check engine light was on. So, ultimately they cleared the codes so I could drive it around to see if the light would come back on. After driving around a while, the check engine light came back on, so, I took it back to the shop to see what repairs I needed to make to get it inspected. The technician recommended that we clear the codes again but for some reason he wasn't able to do it by the computer. While the computer was still hooked up to my car, he unplugged the battery. That finally cleared the codes and I was advised to ride some more and come back. After about 3 miles down the road the 4-wheel drive, brake and battery light come on and those were the only lights on at this point. Not sure what was going on I pulled over making sure my e-brake was not on and pumping my breaks to make sure they were not sticking. Everything seemed fine, so I started to pull off, but when I did the car would barely go although it sounded like I was giving it a lot of gas. It almost seemed like my 4-wheel drive was engaged. With my make and model, I am able to engage 4-wheel drive up to 55 mph so I checked to make sure I didn't bump it by accident. I didn't. After I made it back to my house I noticed that my battery had depleted quite significantly to right at 6 volts. I had to jump it off to get back to the shop I just left. When I got there they started naming off all these different things that were wrong with my car that 30 mins prior were just fine. To keep this as short as possible, I am thinking this is not an extreme coincidence. Is there anyone out there that can help? I'm not sure if something got fried when he unplugged the battery while the computer was hooked up? Any help would be greatly appreciated.