After replacing the headgaskets and enjoying a perfect running engine for a change I decided to check/replace the thermostat on my wifes 96 phase 1 EJ22 but I ended up snapping off one of the two 10mm bolts. My attempt to drill out the rest of the bolt was a pathetic pita and I only accomplished getting a metal shaving in my eye. Subsequently I ended up notching out one of the ears on the pump with my angle grinder so I could get a longer bolt and washer to grab thus holding the thermostat housing in place. It's gone a couple thousand miles so far without leaking but I just happen to have a good water pump from a 99 EJ22 phase2 block. Will it fit?

Yes it will fit.

 

But it begs the question, why wasn't the pump changed out while the timing belt was off for the HG's?

 

I would not put a used pump in.  Not worth the work for the risk.

 

Get a new one, and use a metal subaru gasket.

My wife was paying for the parts. I didn't even want to go with the low cost graphite HG's from Ebay but followed her wishes. Catch 22 situation ya know. Everyone should be married. ha ha.