Well since this post, it's been about 3 weeks.
I have finally picked up a duplicate Rare Sniper Rifle and finally able to upgrade to T4. Which has enabled me to move up in Infamy to the 2800 range. However I still think that the system should be improved with the some of the solutions we spoke of or possibly looking at the algorithm again.
What's more telling is that since this game is being actively reviewed by Game sites and Pro Gamers, their initial reaction is of the same. That the Store and upgrade system is too complex and confusing. I know it's just one review out of many positive ones, but this reviewer hit some key points right on the Head.
Here's a recent review:
https://www.gamereactor.eu/reviews/535423/Battle+Bay/
Upgrading your ship and your gadgets is needlessly complicated, most likely to encourage microtransactions. There are lots of items to buy to improve your chances in battle, and lots of currencies to buy the upgrades with. Sugar cubes are plentiful, but that's the least valuable resource. It's used to train your crew and upgrade cannons, among other things. In order to upgrade cannons you also need scrap that's divided into varies subgroups depending on rarity. You buy this with gold and you can also buy crates with random rewards by spending stars earned by completing challenges. Finally there are pearls, and these are used to speed up your progress. Pearls can be bought with real money.
We quickly grew tired of upgrading our ships and gear as there's so much of everything. Particularly given how mediocre the actual battles are. The whole point of spending time and resources on upgrading and maintaining your ships is pretty much lost as you feel that you've experienced everything the game has to offer after a dozen or so battles. There's simply not enough here to pull you in for a long-term addiction.