If possible, remove the exhaust housing. If the 3-bolt flange studs come out of the exhaust housing, the exhaust housing can be removed without removing the entire turbo, but can sometime be tricky as you don't want to bang the housing around on the turbine fins getting it off. This way there is no chance of that tiny piece of metal getting in there and ruining a seal.
I've always used a dremmel or if you know soeone that runs a CNC or manual mill machine it can be perfectly machined out.