Oh, I don't envy you for the task you have lying ahead.... That's how many of my client relationships start -- a huge ball of inter-related innovations getting ready for release. The topic has come up much here. Let me see if I can pull up a few posts/topics.....
I found
this one. That sets out some of the basic considerations.
The bottom line is this: if a number of innovations are all tightly-coupled as you say, it's often best to write them all into one large patent application. It all depends, though. When I begin to cover a large collection of inter-related innovations, the things I'll need to write start taking shape in my head and I get a sense for whether it makes sense to file one large application (to be divied up later, or perhaps at filing) or a number of applications that incorporate each other by reference. Either way, they all tend to be filed at the same time, so the task is comparable either way.
As an example, one question I have is: if I have a patent application for technologies A and B, and it is obvious that embodiments of these can be combined, is there any situation where it would be useful to write a patent application specifically describing a device that combines A and B, or would it be best to just describe that combination as one of the embodiments of A or B?
Well, be careful about using "obvious" as it's a heavily loaded term in patents.
There are generally two ways to approach that issue. One is to write 2 separate applications, one for each of A and B and incorporating the other application by reference. Each application should make it clear that A and B can be used together. A second way is to write one application for both A and B. You can claim A and B separately and even file separate copies of the same application for A and B, with different respective claim sets for each innovation.
If you hope to claim a combination of A and B, I'd follow the second approach. If the number of claims gets a bit large, you can separate the application into 3 applications with respective claim sets for A, B, and the combination of A+B. The descriptive portions of the 3 applications would be identical, more or less (might change the summary and/or the abstract).
There are many ways to go about covering many innovations in a mass filing. Each has its merits. And, if you hope to get patent protection outside the US, there are other challenges -- particularly in Europe.
I hope that helps.
Regards.