Have you driven enough miles since getting the new battery for the computer to reset the codes? It takes a while for the computer to re-calibrate after a power loss.
I think instead of reprogramming the one FOB you have, they would program your car's computer to delete the stolen FOB. Of course you should then buy a new one so you have spare and then program the computer to the new FOB, and change the lock as well.
So, if you didn't remove the cross-over, you don't need technically need to add one. However, the existing cross-over may not be the best match for your tweeter. But if it sounds good to you, that's all that matters. :-)
Second guess is the starter relay. Third is the starter itself (possibly due to oil leak.)
Check this thread:
(5) 2016 civic starter relay location | 2016+ Honda Civic Forum (10th Gen) - Type R Forum, Si Forum - CivicX.com
My guess is battery. It's start the first time because the battery has been sitting and has had time to recover a bit. When you try start it quickly with no delay, the weak battery doesn't have time to recover.
Do you keep receipts of all services performed? That would help you create a list of services performed and not performed. You would have to manually keep track of when they are needed based on average number of miles or time between services.
When you pulled on the wire in the trunk, did it feel like it moved the mechanism? If so, maybe you need a second person to try to pry open the door while you are pulling the wire.
Speakers can't make the sound that loud if the volume is only at 1%. Sounds like an issue with the head unit or amplifier.
Have you tried reboot the head unit? If that doesn't work, try removing the 18,19, and 20 fuses in the engine compartment for a few minutes, then putting them back to...
Are 3rd party injectors available?
Also, did you try the simpler solution of changing the plugs and coil? You can swap 2 plugs with the coil and see if the misfire error moves with the plug/coil.
Check the voltage to ground (to a bolt on the body of tbe car) of each pin when the light should be on. (Bulb disconnected.) It should 12-14V for each pin but one, which is the ground.