Okay, here's what I think it is:
A late prototype Macintosh. This was probably used by a Mac Team member who kept using it for a few years after the release of the Mac. As it was a daily use machine, it was upgraded as they went.
What's original? The case, frame, floppy drive bracket, floppy drive, logic board, ROM chips (342-0220 and 342-0221, right?)
What's new? The DRAM chips, the mini-mux board (the little "extra" board on the logic board at E3).
The mini-mux and 256kbit DRAM chips were a popular upgrade back in the day. If you wanted it to be "original", you would remove the mux board, repair the cut trace on the bottom of the logic board under the mux board area, and replace the 16 DRAM chips with 64kbit chips.
I'm a little surprised that the ROM chips are still the original 128k/512k versions. Many people upgraded these to the Mac Plus ROMs which added 800k drive support giving you a Mac 512ke.