The 6.9 heads are actually drilled to just under 0.500", which means they will pass a 1/2" threaded rod, but not a 1/2" bolt shank. Also, by time you have all 17 bolts and position tolerances to worry about, something isn't going to line up. So I just reamed the holes to 17/32", and everything worked fine.
I am using Classic Diesel Designs turbo kit. Which is essentially a stock 93/94 turbo setup with a few ATS pieces thrown in. I am still running the 6.9 pump (or whatever pump the Ford dealership in Lafayette, IN put on it when the original went down as I was passing through town 6 years ago.) Injectors are from Accurate Diesel, but I have a 2nd set from CDD on the shelf incase I throw a bigger pump at it.
The pump is definitely the limiting factor right now. I don't have it turned all the way up, but it is close. Very little black smoke at load, and EGT's rarely exceed 1000 F, the temp probe is in the passenger exhaust manifold. Peak boost is about 10 psi with the waste gate blocked off. I also had Oregon Cam grinders regrind the cam.
I would suggest running the turbo rotating assembly regardless. The heavier wrist pins and rods are just good insurance.