Welcome to the forum, BootsWalker. We're glad to have you here.
I think I can answer part of your question but not all of it. You have a lot of javascript links that are of the type that phpdig does not follow. Check the
Phpdig Features in the documentation and you'll see what I mean.
There are other plain old href links that I think phpdig would follow, unless there is a limit on the URL length, and I wouldn't know anything about that. Perhaps that is the reason those pages aren't being indexed.
Hope this helps.