Sounds as though there's more going on than possible floppy drive issues.
At this point I'd suggest testing the following simple as possible configuration:
- v40.68 (OS3.1) ROMs fitted
- A3640 CPU board fitted (both main board clock source jumpers need to be set to EXT)
- Both floppy drive and hard drive disconnected from the main board
- No expansion cards fitted
As above with nothing else connected to the main board except the power supply and the monitor, when you power on the machine, you should eventually get the purple 'insert disk' screen after about 30-40 seconds (of staring at the black screen). At power on, the power LED should change brightness once. If you see it flashing as you described, then you probably won't see the 'insert disk' screen, and there's some other hardware problem preventing it from booting.
At this point if you have boot problems, remove all 4 fast memory SIMMs (the 4 nearest the outside of the board), leaving only the innermost chip memory SIMM present. Repeat the same tests above and see if it boots or not. If so, you might have a bad fast memory SIMM.
Also try a known good chip memory SIMM if you have a spare (specifically needs to be 2MB, double sided). As the memory tests in ROM aren't thorough, it can try to boot (and fail) under certain failed memory conditions.
Else there's probably some kind of hardware issue with the main board. At this point DiagROM would help to see more of what's going on. The latest version of DiagROM (v1.3) includes good chip memory tests. If that doesn't narrow it down, then you could send it to me for repair. I have a run-time hardware debugger that shows the detail of what's happening internally to see where the ROM software is failing, in order to narrow down what area of the hardware is causing issues.