I have only done one on a stock turbo, but I am getting ready to enlarge the waste gate hole on a P trim exhaust housing.
First you need to check the alignment of the waste gate puck with the existing hole.
(a) Take exhaust housing off turbo and bolt to down pipe.
(b) Hold puck against the exhaust housing and through the housing outline the exhaust waste gate hole on the face of the puck. I covered the face of the puck with machinest blue and used a scribe to mark the puck.
(c) Take down pipe off and check if puck is centered on hole. If it is not centered you will have to enlarge the hole to one side so it is centered on the puck.
(d) I ended up (on the previous turbo) using a waste gate hole which was 1/4" diameter less than the puck. This provided 1/8" of contact around the edge of the puck and the hole.
(e) Scribe the outline of the new hole on the face of the exhaust housing. [Check at least twice to make sure center of scribed hole and the actual puck are the same].
(e) I used a carbide cutter on an air grinder to enlarge the hole, I do not think a drill bit would be the best tool to use. An end mill would work better than a drill bit.
(f) Enlarge the hole out to the scribe marks, keep checking to make sure you are not grinding outside the scribe marks.
(g) Once the hole is enlarged to the correct size, you then need to taper the inside of the exhaust housing to the hole. [Do not taper or radius the hole edge at the housing and down pipe face]. I used a round ball grinder bit to taper the backside of the exhaust housing.
I hope I have not left anything out. I am sure others will jump in and add to what I have said.
Take it one step at a time [it is like eating an Elephant].
Deep Enough
Donald McMullin