Hmmm, that's bad luck.
Hope your Blizzy isn't really dead - I'd like to think maybe the rebuild process has disturbed the connection between that & SCSI module (not too secure on mine) - does it work with the SCSI module removed..?
Poss about to teach grandmother to suck eggs, so apologies in advance:
Your video issues remind me of a poor connection somewhere...
-Indy to mobo: Mine's a d*mn tight fit - lots of force needed to get it to seat, could your's need an extra shove? Also you may have noted that 'dodgy-looking' cut out of the side of the socket which is to allow room in certain mobo revisions for a resistor (I think) - could this be your issue? Not enough of a cut so the socket isn't fully seated no-matter how much pressure applied..?
-Indy to ribbon cable: secure?
-Ribbon to VGA: secure?
-VGA to VGA lead: Not seating well? The reason I ask is I mounted my connector in the plastic the exact same way it's done with a PC GFX card - The 'nuts' either side of the connector holding it all together... Thing is the plastic is a lot thicker than a blanking plate so they were preventing the cable from making a good connection. I had to counter-sink the 'nuts' a bit.
-GFX drivers: I'm using the HighGFX drivers with mine - the v40_6 released for the Indivision made my display go 'all to sh*t'. The v40_5 works fine - similar issue for you? (won't explain games of course)
Prelude: I don't own one so apologies if I'm way off: Clockport header? AmigaKit stock extender cables / risers for such difficulties. More expense, I know.
Bah! alexh does in one line what it takes me an essay to explain!