I hate to be contrary, but I'm not so sure I like the new method of upgrades. Before when you selected "Upgrade" no components would be removed, but after the latest patch selecting "Upgrade" will remove all but the jewelry. Supposedly this was because some people had difficulties finding and removing the non-jewelry and the linear strip (below the 3D window) that displayed the actually components was somewhat erratic.
My problem is that sometimes I'm just doing an upgrade to, for instance, change out the engines to get more speed. I don't want to have to remember (or write down) what weapons and other components were on the ship so that I can re-add them as part of the upgrade. Getting the components wrong also adds to the cost when you upgrade one of your ships on the main map. Doing this "minor mod" was easy before, but now it's a longer process with more chance of error.
What I'd like is that when I select "Upgrade" a pop-up appears and asks "Keep existing non-jewelry components?". Answer yes and it works just like before the patch, answer no and it works like after the patch.
Just a thought