Well, the good news is - the update worked. Otherwise, well... I made a very spicy purple meatball. (
https://imgur.com/a/KN8ISxF)
The quality upgrade menu also strips the common upgrades already installed just by opening a ship in it, and does so without any warning. I think it would be better if you can make the mod calculate them retroactively (as in, give the same end numbers for any sequence of ship and quality updates), which then will make it easier to use the mod - no need to think what you have to upgrade first, you can upgrade anything and get there eventually.
One thing that annoyed me from the first iteration of this mod is that you can't see the upgrade quality of the mothballed ships. In fact, you can't know the upgrade quality until you open the ship in the upgrade menu. I suspect the way the mod works is that it keeps track of ship's API - which doesn't change with reloads or exploding of the battlefield - but does the check only in the menu, and doesn't keep track of any upgrades that were attached to the ship (and thus they are lost when the ship explodes). If you can make the mod show the upgrades without having to open the menu - say, when you look at them in the market - and make losing upgrades after ship's death an option, rather than an inevitability, that would make using the mod easier.
Other small changes I think are appropriate:
1. Change the ratio of upgrades for destroyers and cruisers to 6.66% and 5.33% per level respectively. Right now they get a shadow buff of 20% at full upgrade level, and they really don't need it (combined with up to 50% upgrade buff from quality as well). I mean, right now the whole mod makes ships OP, making some ship classes even stronger will just make any attempts at balancing harder.
2. Change the ratio of resources needed for upgrades.
I suspect it wasn't updated since 0.7, and after the economy changes the values and quantities of many resources in the market has changed dramatically. My pet peeve would be volatiles - in 0.7 they were on the level of metals at ~30 bucks and quantities easily above 1000, in 0.9 they are at ~250 and with quantities of 100-600, rarely more. I think heavy machinery is also affected (nowadays it's needed for exploration as well), but I don't know the numbers.
The more I think about it, the better the just-buy-it-with-money option sounds. Will have to limit buying upgrades to work only in ports, although that doesn't sound like a bad idea - as is, with the amount of resources required, I rarely if ever find myself upgrading ships outside of friendly harbors.