I couldn't find a trace of the other two, though looking at your account (or what I think is your account) I am seeing a slew of filtered posts, some of which are on topic, some of which are not. I just approved a couple of your most recent on-topic posts, however I can tell you that you will need to keep a good ratio between your own site(s) and other good content for the spam filter to go easy on you. It filters really heavily against people who submit the same domain a large part of the time, and we (moderators) tend to stick to that as well.
I will comment on your other points in a little while.
EDIT: Okay, now for the rest.
I think the warm fuzzy memories you have of proggit are akin to the warm fuzzy memories a lot of people have of reddit as a whole 3 or 4 years ago. But with a larger userbase comes a lot of noise and idiocy. In my opinion, /r/programming was one of the first subreddits to take real action against quality decay. There was a period of time, after the heyday, but while /r/programming was still a default, when rage comics and advice animals were rampant. Maybe not quite as rampant as the rest of the site, but it was pretty bad. There were lots of people who were not programmers submitting and commenting, so lots of stuff ended up being off topic.
I think the quality has improved immensely since then, and I think this is in part due to strict moderation and the disabling of self posts. I will allow that it certainly isn't as great as reddit as a whole was in its heyday, but it's getting better.
There's not much we can do about the comments. We can't moderate comments for stupidity (because that would be pretty messed up). The only thing I've ever moderated comments for is spam and personal info.
A reboot, unless it's in the form of a different sub, is probably not going to happen, but I'd certainly be interested in hearing any ideas for improving the subreddit in its current form.