1), 2) and 6) Good idea, I'll keep these suggestions in mind
3) Renaming the speedups is a good idea, but I'm not sure about the overclocks as both their durations and multipliers change. I think "10-minute 1.5x overclock" is a weird item name lol
4) Right now terraformed mines mine infinitely, despite the game saying otherwise, but once they do have a limit I'll make sure to include more information
5) There are overlays, the annotator and bookmarks that you can use to quickly go to where you want. I don't think it's a game of "Remember where all your stuff is", but rather "Remember to use the tools the game provides you to not have to remember where all your stuff is".
But I agree that a list of all the systems that contain stuff and other things you mentioned could be useful too