I understand completely- I have SO MANY plot threads that have gone unresolved and I've forgotten about (such as Sharkticomics Soundwave and Swindle). I've actually toyed with the idea of a fan fiction that chronicles their attempts to return to Sharkticomics.
[part 2]Another example is that, in my first appearance, there is nothing in the comic that says that Crosshairs is LegoTFGuy, just a side note after the comic. As such, the humor of my line about Scoop wanting to ban Bronies is lost on the audience the first time they read it.
Also with this is the fact that you haven't established anything about the MMS or who is a part of it, despite that being the main concept that the comic is based on. A better intro comic would have you talking to me and Warpshard about something to do with the MMS, including plenty of name drops so we know who's who.
[part 1]I think it's biggest flaw at this point is that you don't introduce the character's personalities, but rather just have them in some random situation. Some personalities parts are implied- such as your cracks at Kup for being an old fart. But beyond that his personality needs to be developed. The most important thing to remember when story writing is that the audience doesn't know everything about the characters- you need to explain it to them. (Also, unless Kup being old plays a major part in the comic, I would have suggested making a different first comic that establishes the setting and using the Kup gag later.)