Here you go - this is the shaft alignment bushing in the log to set the gear mount coupling alignment on my boat. At the same time we do a "rough" alignment on the far mounts for the coupling flanges and measure out the clearances on the cutlass bearing. Then this alignment bushing gets pulled, the seal assembly installed, coupling installed and pulled up and mated. Finally, the far mounts are adjusted to close any alignment gaps on the couplings and you are done.The mount adjustments nearest to the coupling flange on the gear are to center the coupling flange with respect to the shaft log to ensure the dripless seal boot is not tweeked to one side. Those are set when the shaft is installed and the seal boot not yet in place to center the shaft then they should never need to be moved again unless the boat is taken apart again. Setting those are always out of the water with the log open. The motor mounts on the other side (furthest away from the coupling flange) are what are used to move up, down, and side to side to align the mating faces of the couplers.
Now - on the flange faces - both faces are machined parallel to ensure the bolt heads are not angularly loaded. So, do the TIR with the bolts tight and do it again with them relaxed comparing with the TIR on the shaft at the seal area. You will then know if the coupling is deflecting the shaft.