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IRQ conflicts will be caused by the new card taking up different allocations than your computer is used to, it very seldom happens nowadays, but happens nevertheless.
If you go into device manager and to the item that is yellow-flagged, right click and go to properties, then go along to resources, you should be able to manually set the irq (i think this only happens when it detects a conflict). Change it to something that hopefully won't conflict with anything else.
From your original post, the first thing i was worried about was damage to the AGP slot on your mobo, i'd be checking that out very, very closely. But it seems as if it's worked without any troubles. So from there, it sounds like you mashed your gfx card :<
Look for any physical damage on the card itself, since your mobo seems undamaged, it's likely that the damage is around the connector for you screen. I'd be tempted to test it on another computer if possible - might still be partially useful (for your server etc).
All-in-all, i'd say you got away with murder there, that could have been catastrophically bad.
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