Finally. I have succeeded after much reading and trial and error to create my own custom firewall and more importantly QoS script. I have revisited QoS several times since I lost my Shorewall config to a hard-drive crash at work. I endeavored this time to build a QoS script from the ground up with no 3rd party software. This proved a little more difficult and time consuming than anticipated.
The very high level break down of how it works is this, IPTables is used to assign port, destination or source based traffic arbitrary marks. These marked packets are then read by traffic control (tc) and put into designated Hierachical Token Buckets (HTB) which have assigned rates and priorities. That's the gist of it.
It all sounds quite boring and simple but I assure you it wasn't that simple and boring is a subjective label. It's exciting for me because it is the final piece to the SNAP (one of my pet projects) puzzle.
If anyone is interested in these scripts, let me know and I'll make them available.