Hey Amanda, I think he's probably just little...he was actually extremely fat up until about a month ago...and he weighed 2 1/2 lbs. Within the last month he gained 1/2 a lb and he got a little longer and taller, and filled out to a more "ideal" weight. When he was 8 months he was like an 8 on that weight chart they use at the vet...
When I took him for his health check he said he had moved down to a 5, which is a good ideal weight for him. I don't know 100% everything about nutrition, but I've always been told to be careful with the tinies about putting on too much weight, because being chubby can actually be a bad thing since they are so little. I was happy to see he had finally come down to a 5. Like you said, I do free feed all mine and they have about 6 bowls throughout the house that they just run around and get some of random times throughout the day when they want it, so I'm not sure about scheduled feedings with the little ones.
Oh and as far as vaccines, nope he only had three as a puppy and he had one more at 1 year old, and a rabies at 8 months. So nope not that many. I was always so afraid to put him under so I was waiting for him to turn 1 year to get his retained teeth out and have it done at the same time and I was dreading it. I use Petzlife on all mine, the gel and the spray. I know his daddy's teeth are fine, I never saw his mom's teeth. I worked for the lady where I got him for awhile, so I had him picked out when he was only a few weeks old. I know they're both healthy dogs and their lines are free of diseases, but I guess it's hard to tell about their teeth...
