Kenshi said:
1. Even with Capt. Norwood's reference in the KS handbook, our story line takes place in 2654, two years prior.
Well, keep in mind that Capt. Norwood's reference in the KS handbook isn't a case of "here's this pilot who just graduated" - in fact, it says that she's looking forward to retiring

. So, this would mean she was around in 2654.
Also, while I love the Wing Commander Movie (I own both VHS and DVD copies), I personally don't consider it nessassarily canon. [...] If we incorporate your thoughts, GREAT! If not, well, hey...
... you're getting a free comic out of the deal.
Well, as someone who's worked (and is working) on a few fan projects, I can understand exactly where you're coming from. As I'm sure you'll learn soon enough, it can be very frustrating working on a project like this - there you are, doing your best to make something people will enjoy, and all they seem to ever comment about is how some insignificant little detail doesn't match what's said in some obscure source

.
Here's my advice, however -
listen to them

. It doesn't matter what you think about the source they're talking about - you may not think it's canon, but somebody obviously does, and that somebody is your audience. The WC franchise is a bit unusual in this regard - for most big franchises, you have the ordinary fans who will enjoy any (good) product as long as it's from that franchise, and the hardcore fans, who would like everything to be consistent with previous products. But in WC, we are all hardcore fans - the franchise has been on ice for half a decade, and so all the ordinary fans have either left or gone hardcore.
So you need to take into account that your audience is going to be very demanding in the canon department. It's best to be flexible - for example, in the case of these two callsigns, if people have some objections to their validity, does it really hurt your comic if you listen to them? I mean, unless you have a big callsign-dependent plot point, it won't adversely affect your comic, and it will make things easier for you (because you won't have to waste time arguing about why these callsigns are a good idea after all

).
(and don't worry, you'll find that on the things that matter the most for a comic - visuals - the fan community will be very accommodating; for example, there are no less than four visually-different uniform/flight suit designs from 2654, so nobody will be especially offended if you come up with a fifth design)