Rather than bother you guys with crazy specifics is there a quick guide or troubleshooting steps that you reccomend? Or anything you have done with your site when facing subscription issues? My stuff seems real intermittent.

I am not aware of any issues with Active Forums subscriptions. Most of the time the problem lies with the mail server, not with the module.

Usually when hear of intermittent email issues it is related to SMTP server configuration. The first thing you want to rule out is if your SMTP server has a max number of connections/messages per hour or some other interval. Almost all hosting/email providers do this now, but won't give you specifics unless you ask. The next step would be to see if it happens for all email accounts. The best way to do this is to subscribe to a forum using multiple accounts that have email addresses on different domains. We haven't run into any SMTP issues that weren't resolved after going through these two options.

Real quick though - is there any sort of logging for emails sent?

If you have the Mail Queue enabled for Active Forums you will seen entries in the scheduler log that will tell you how many messages were sent. Any failures are logged in the event log.