AAAAHHHHH!
So i resoldered everything again, and then hooked up the system without the hdd or dvd drive (ie, just the motherboard). And everything worked. the system booted fine. 2 LEDs on the X3, blue light on the front panel. Everything was normal. So i threw everything back into the case and tested it one more time before screwing down the top cover: and was back to the beginning. Just a normal Xbox boot. only 1 LED on the Xecutor. No light on the front panel.
I have now checked every LPC connection at least twice, paying particular attention to 6, 9 and 15 (which are the 3.3 and 5v connections). Still no success. I'm starting to wonder if my modchip is dying. I didn't have an insulating sleeve around the ground pin on the X3 for many years (just some electrical tape), so it's possible that the chip shorted out and isn't working for that reason.
But the fact that I had one successful boot today is driving me crazy, cos it suggests that it's just a matter of poor soldering.