#1 - For the instrument rating requirement, see 14 CFR 61.65(d)(1) which states:
(1) Except as provided in paragraph (g) of this section, 50 hours of cross-country flight time as pilot in command, of which 10 hours must have been in an airplane; and
You can still tally your cross-country time total. However, you will need to make sure that any cross-country flight time you use towards the instrument rating be PIC. For instrument certification, I would use a spreadsheet and log out all the flights that do qualify, print it out, and keep it in your logbook. If and when the examiner questions your cross-country aeronautical experience, show them this sheet, and you're good to go.
#2 - If you can't reconcile these flights, personally, I would take it as lost time. Otherwise, you would be in violation of 14 CFR 61.59.
#3 - You can leave it blank.
#4 - Yes.
Don't feel bad about any of this. Lots of pilots I know have experienced at least one of your issues, me included. Just do the best you can in the future.