The whole thing was a pain to put back together with the new turbo. I fudged it every way that I could just to get the downpipe bolts in. Exhaust hookup was part of the equation so I'm going back at it without exhaust and then do what I need to it to compensate.
But looks like my main question was answered in that the change of turbo should not be an issue. Wanted to get that out of the way first.
Turns out that there was a small difference in the hole to hole distances. Also my new cap screws have a slightly larger diameter. I drilled out the 8.75mm holes to 10mm. Now getting .115 clearance and puck position is good. Think that's enough? Could get a little more if I remove header to turbo gasket or could put a piece of Helix insulation in there.
One things for sure, going from a TA-49 to a PT6466 with a THDP, you have a lot of wastegate hole porting, contouring and blending ahead of you. Should be around the 1.15" mark. You won't have any boost control with the stock as cast hole size. It will creep and not stop so be ready to get out of it quick. Don't forget to smooth the transition on the inside of the housing where the hole starts. Give the exhaust a smooth transition into that hole, vs a sharp 90° turn.
Hope this helps.
I see many in this community who never ring out their current turbo and switch to a bigger one in search of more power. The bigger turbo now has to blow through the same restrictive engine as the smaller turbo did. Now the new problem is the inability to run lower boost numbers. Then modifications are done to allow lower boost. There is another way to fix the problem and that is to run more boost.