Oh, you have a Service Manual? I would like to help more, but there is only so much I can guess about without leading you on a wild goose chase since I don't have the unit in front of me, and if some controller is fried, might not be able to figure it out even if it were in front of me without more knowledge than I have about these units.
Highly integrated units can be a PITA, is one reason that I, like people who build classic cars, like to keep them simple and in the case of audio, build a separate amp that isn't married to the input sources. You don't get a fancy display or remote that integrates *everything* that way, but then when something goes wrong, easier and less expensive to replace modular components.
You could try asking for help at one of the electronics forums, for example this one:
Discuss any audio related topics in this category (amplifiers, speakers, etc...)
www.electronicspoint.com
As far as your CD tray opening and closing, it might be a bit controversial but I would pull the entire CD mechanism out of it, and instead, get one of those inexpensive USB/mSD, MP3/flac/etc audio player modules on ebay/etc, tap into a low voltage rail off the PSU to provide 5V through a linear regulator like LM7805 to it, and use its output into the existing line level input from the CD player you removed. Just saying that CD players.... meh, when you can fit an entire bookshelf worth of CDs on a tiny mSD card, they have outlived their usefulness except as an archive media.