Is there a quick way to quickly disband a group of units that you have bound to ctrl + 1, besides having to ctrl + 1 ctrl + 2 ctrl + 3 every unit thats in the group? Also, is there a way to delete red/green/blue waypoints?

Hi. Still having fun blowing shit up? Same here :)
Ungrouping of Units:
I found no way to do it other than the one you mentioned, meaning re-assigning individual units to groups.
In the end i gave up on the groups entirely. The lack of info regarding the individual units when grouped and the difficulty of issuing orders to a specific unit in a group makes the grouping feature pretty useless to me.
I use the follow command instead to keep my units in a 'bunch without having them in a group.
Removing the colored waypoints:
I also didn't find a way to do this.
After a colored waypoint route has lost all usefulness, i delete it by placing a single marker of the same color, and then i drag that waypoint to a corner of the map to keep it out of the way. It's not ideal but it was the best i could come up with.

Ah it's too bad, because it makes the strategic part of the game feel a little neglected by the devs. Otherwise, it would be perfect.

Well, it would be nice if the groups worked a little better.
But i'm already used to using the follow command and i almost don't feel the need for groups. If the number of units was massive things could get messy, but as it is, it's not bad.
And the action makes up for all the little quirks.

Hotkeys:
1 q z 2 q z 3 q z
lol it's also quite irritating when sometimes units don't follow you. It's alright when you're in an aerial vehicle, but when on land vehicles, units take longer than expected of them to tag along. But you're right, at the end of the day, all the boom boom bang bang makes up for all other shortcomings.
Still being a perfectionist, I wish they'd released the patch before Interplay hit the wall