Turbo intake clearance of water pump bolt

I started a new thread for this since my old Hahn Turbo Install Questions thread was getting hard to follow.
I just tried installing the rubber 45 degree boot that connects the turbo intake opening to the air intake tube. Unfortunately, the turbo intake opening is so close to a bolt holding the water pump in place that I'm having trouble getting the rubber connector to fit onto the turbo air intake opening. Here's a pic - (the shiny stuff over the turbo intake opening is tape holding a paper towel to block anything getting inside the turbo) -

As I mention in the pic, using a file small enough to fit into the gap between the turbo air intake and the water pump bolt to file away material from the water pump will take a long time. I'm considering trying to loosen the 4 bolts holding the turbo to the exhaust manifold and the 2 bolts holding the Wastegate to see if I can free up enough space to fit the rubber boot over the turbo air intake mouth and the water pump.
Anybody have experience with a similar situation?
It's very frustrating to be so close to finishing and experiencing these small holdups.

When I tightened the bolts according to the instructions, I was concerned then about the tight clearance.

Quote from iNewton

I would check to make sure the headers are sitting flush with the block.

Did you forget to put the exhaust gasket in place when putting the log header on the engine? That would move the turbo closer to the block if the gasket is not present.

If you loosen the 4 bolts holding the turbo to the headers do you have some play to work the turbo a bit?

Since the turbo is connected via the 4 nuts holding the turbo to the bottom of the manifold and the 2 hex key bolts holding the watsegate to the top of the manifold, I guess I'll discover if loosening those 6 fasteners will let me install the rubber 45 degree boot to the turbo intake throat w/o having to redo the turbo/exhaust install.
Looking at the pic at the beginning of the thread, it looks like the gap between the water pump bolt and the turbo air intake throat is about 1/8", but the rubber boot is closer to 3/16-1/4".
I'll post results if loosening the bolts works.

I tried loosening the 4 bolts securing the turbo to the manifold and the 2 bolts securing the wastegate to the down pipe and the bolt securing the bottom of the Hahn Street Race muffler, but still needed a little more clearance for the boot. I used a Harbor Freight variable speed oscillating tool and a metal-cutting blade and lightly trimmed the water pump bulge where indicated in the first pic and then used an abrasive tool on the oscillating tool to try and smooth the cut, following up with some sandpaper. Installing the 45 degree boot to the turbo intake then went smoothly. I re-tightened all of the bolts I loosened and installed the hot and cold charging pipes and BOV. Tomorrow, I'll hook up the various vacuum tubes and remove the Top so I can then remove the dash cover for access to hook up the Innovate SCG-1 Boost/AFR gauge. I hope to finally be able to test-start the engine in a few days if everything goes smoothly.

I seem to recall reading somewhere that some folks running the Hahn setup preferred the Alpha reflash. I assume Bob reflashed my ECU with the Hahn setup.

Now, my main concern is verifying that the oil pump is actually pumping oil. I'm trying to figure out how to use a pre-luber and hook it up to the Ecotec 2.4L engine. Here's that thread - Question about oil pressure when starting engine after several months of non-use