[asphaltgambler]

I need to say this, please dont take offense. You are way down a rabbit hole at this point. Something's changed since the initial work. As Fred has asked, something pinched or connected/ cross-connected. You may ( have created) a CAN bus problem when reassembling through human error.

It's odd the car sat for a few days and the battery died. In that situation the battery may be in an extreme low state of charge- it appears dead but still has residual voltage so all capacitor memory remains.

We've all been there. All of us that do problem solving whether it be mechanical or say, mathematical go off path. It's hard to get out of that. From your posts it seems to me some basic testing by eliminating ( with absolute certainty) has been guessed or not completely ruled 'yes' or 'no'.

Have you considered a second opinion by expert diagnostic guy with a Pico scope?