My input is that if you're worried about the ability to make a pipe tap correctly, you should have picked a different project.  But then, if you have Steve working on it for you, allowances have to be made....  :^)

Seriously, though....You get the best readings in the manifold, so put it in the manifold.  Why bother trying to "rationalize" why you think the readings you're getting are "close enough" to reality, when it's so easy to just get accurate readings?  At least that's the line of thinking I went through with myself before I put mine in the manifold.

I used the boss where the front-most mounting bolt for the rear (starter) heat shield went into the manifold.  I put a 1/4" drill through at that location (clearance for the pyro probe I had) then followed that up with the drill and tap to proper depth for the npt compression fitting that holds the pyro probe in my case.  Lastly I drilled the forward mounting hole in the heat shield bigger so that it could be captured by putting the npt fitting through it, rather than the bolt as was original.  This locates my pyro probe between the #3 and 4 exhaust branches to be sure and capture exhaust temp coming from the rear two cylinders where my mechanic friends tell me most diesel problems surface (in the form of head gasket leaks from overheats).

Another tip from Warren to help with heat issues was to move the water outlet fitting from the left side of the head to the rear of the head.  I did that on mine before I put the motor in.  Used teh same hose that used to go on the left side, just put it on the rear and then used a metal elbow to go toward the heater inlet.

-Dave G.

PS - I had my exhaust and intake manifolds ceramic coated too.  Didn't bother with the turbo or the downpipe.  My underhood temps seem very cool, at least not noticeable at all when the hood is opened after a long run.