Note: While I'm quoting people, I'm editing some of the quotes to read "*snipped for length*" for the simple reason that I don't want this post to become an immense Wall of Text that is scientifically and medically proven to cause ocular hemorrhaging. It's not in the least bit meant to be derogatory to the people who made these posts.
The disadvantage of the Borg is primarily that they work on exceedingly slow timetables, especially considering the relative strategic mobility advantages they enjoy over contemporary ST powers. Transwarp is much superior in traversable capabilities than warp drive, yet the Borg have not used this to explosively multiply.
This could easily be put down to the fact that their industrial capacity simply cannot keep up with the exponentially increasing volume of space they control, and the proportionately exponentially increasing volume of space that is open to assimilation; in fact, I'd consider this to be the case.
Since they are effectively stretched to (relative) capacity, only able to send (relative) token force to assimilate prospectively useful species in (relatively) far-off corners of the galaxy, then it's likely they would dedicate only a single cube to the assimilation efforts of any new 'verse they are now able to move into, for the simple reason that they are already prioritized into assimilating the galaxy they reside in; they simply lack the ability to manufacture new cubes (or fleets of said craft) to assimilate new territory because all current shipbuilding is either exceedingly slow (unknown) or their shipbuilding is already operating at near-capacity (likely).
With the added issue that their current fleets are needed where they already are; each fleet might be able to spare a cube or two, but it's likely that that's it.
I personally advocate the dimensional tangle being the Borg's fault, because it actually fits quite well with the character of the Borg. They've done it before, and if they stumbled upon a piece of tech that gives them the ability to do it easier than ever, then it's a case of them obviously doing it, given their previous history. They'll (probably) be a lot more wary, given their previous experiences with said fluidic space. But they'd totally do it.
WRT release, my advice is to simply put together a list of the mods you've taken assets (models, sounds/music, particle effects), and then post in the threads for those mods your request. I myself made a request regarding the use of the Venator-class mesh (in part with modifying it in mind), and it was granted to me so long as I included credits for the original modeller.
I personally see no problem with the setup of two distinct mods; however, I'm thinking that there might be possible merging/stacking issues in the future. However, at this point I'll say that that's something we'd have to figure out when we get there, if there even is an issue.
WRT tracking the changes, changelogs are your friend. This is also why you should make a "version history". The current version you can appoint as "0.1". Go through and list all the changes you made, and then for version x.y (where x.y is the version number), you add whatever new changes.
-blah blah change 1
-blah blah change 2
-blah blah change 3
-blah blah change 4
-blah blah change 5
Naturally, replace "blah blah change x" with whatever you actually changed.
An interesting idea. While I personally consider the Borg-found Q-tech concept that's been tossed around the last couple of pages to be better, I think that we might be able to weld this together in some way.
Off the top of my head, maybe the Sith had said brane-rupturing project in order to expand their power&influence (as the Sith are wont to do), and it's not been doing so hot; then they find a portal that leads right into Federation territory (said portal is a side effect of the Q-tech&Sith experiments). That brings the Federation into the war, while the Empire is confronted on two fronts; their own invasion of the Federation and Borg assimilation on the frontier.
I wonder if the guy who did the Sci- fi crossover mod for Empire at War forces of corruption had this much trouble?
Marvel vs DC Comics short stories are very popular you know.
Most crossover stories tend to use what amounts to thinly veiled authorial fiat for the crossover mechanism; it's not about how it happens, it invariably tends to revolve around the aftermath and the repercussions. That said, 99% of readers don't care that it amounts to thinly veiled authorial fiat, because they tend to care more about the repercussions and aftermath than the "how they arrived here".