Back to square one. At least I know what won't fit

Using the previous pieces as a template, I recut my shapes:

This time, however, I left a tab on the motherboard tray:

Again, using the old piece, I line up to see where the lip for the amplifier shelf was located:

And cut it out:

So here are my two new pieces:

And this is how they will fit together - the tab will act as the rest for the amplifier shelf:

I once again rebuilt the motherboard tray with the back wall brace and the MDF standoffs:

The holes were crack-filled and the entire assembly repainted.