I find it quite amusing that you reference the military/Genius Patrol wanting a Honor Harrington instead of a Sonia Hemphill when in the Honorverse the reason Manticore (Honor and Sonia's star nation) experienced long term actual strategic success was because of Sonia Hemphill and the rest of the R&D military people continuous efforts on R&D. Sure, Honor is the titular MC and hero of the series but the main reason she and her nation ends up winning is that space warfare is changed with the introduction of starfighters, extra large barrages of longer reach missiles and finally longer range precise targeting thanks to FTL communications. Oh sure, Honor helped develop some of the tech I just referenced thanks to her incredible tactical and strategic knowledge and experience and was the one to use them on the battlefield. But the actual development was not done by her.
And would you look at that. This fic's MC is supposed to be Sonia with the tech uplift, not Honor. They even have some paralels given it is also a story of conflict between 2 insterstellar nations with some very different characteristics such as size, culture, tech development, etc...
I'm not familiar with the setting so I can't really comment on the whole issue with the dates, though if it is correct and there is less than 2 years before the next war then all our speculation is pretty much worthless. Because as you said one does not create, prove, test and start to market a new enhanced FTL drive technology in less than 2 years. Which means all her efforts so far are gonna taste like ashes in her mouth, since she didn't change a thing since she started her journey more than 5 years ago. Now that would be quite a kick in the teeth for her.
Actually the one thing they probably can get off the ground is the FTL comms. Which on their own present a massive advantage in knowing when the enemy is coming in and having a week to prepare because you know they jumped and got word before they got to the other end. The black boxes can likely be deployed much faster but the HPG will also be prioritized simply for the raw advantages it can bring. Even in the unlikely event that the military doesn't immediately grab it with both hands the corporation WILL.
Someone in the real world spent about $300 million to put a private fiber optic line in a straight line between New York and Chicago because it gave a few milliseconds advantage on trading futures between the New York stock exchange and the Chicago exchange (VERY valuable). What would a Corporation do for a 1 week (edit: Minimum. Assuming only one jump. Multiply by number of jumps) time advantage over their competitors?
Edit: I thought I would take a moment to expand on this. I am not just talking about stock market manipulation here. Let us look at logistics for a minute. If you are 6 jumps away from someplace and you want to order something it will take at least 12 weeks to get it to you. 6 to fly someone there to make the order plus another 6 to get the order back to you. and that assumes the item is in stock and the ship it is traveling on makes maximum haste back to you. This is the same with information gathering or any other activity.
If you have ftl comms at both locations that time is immediately cut in half for physical goods. You can make the order the same day you realize you want it and the people at the other end can immediately start working on getting it to you. If what you want is information, then the answers are far faster.
So lets pretend that earth is the center of culture and you run a store that is the subsidiary of megacorp. A new fashion trend/toy/game craze takes over earth and starts moving outwards. Headquarters on earth finds out in real time and sends out a bulletin to all stores. Stores review and make purchasing orders in short order. The bulk order starts making its way to your store 6 jumps away. Everyone else is in the dark. The news will take 6 weeks to get to them due to jump times.
6 weeks later the news arrives. And so does your order. The day the new fashion trend/toy/game hits your world you already have them in stock in your stores. Your competitors will have to wait 12 weeks for the round trip order before they can have it in their stores.
By the time their orders arrive you have already sold everything you have and have more on backorder. Backorders you were able to "fax" in the same day. Edit 2: depending in when you ran out of stock you might be able to get the second order delivered before your competitors get their first order in. Massive Profit. Your competitors are left with what few people were not able to buy in the first (and possibly second) wave. Too bad. So sad.
This works for everything. You know the price differences between systems and know where to buy low and sell high before you ever calculate a jump. Do you know there is a shortage of metal/widgets/lefthanded screwdrivers on some critical project on Planet Krishna? You can have negotiations before anyone else, and you can have it there in half the time your competitors would take.
Empires are made with advantages like this. Their competition will make a move and always find Megacorp there first. They wont just beat the competition. They will crush them. Those who have access to FTL comms will run roughshod over those who don't. And they are not stupid people. They won't give this advantage up lightly.
And now the government that could have controlled this from the start is going to find themselves having to give concessions to the Megacorp. Concessions they would never have had to make if the genius patrol had just set her up in a government lab somewhere.