Update: Resolved.
I thought I would provide an update incase anybody has a similar problem or is just looking for insights.
I went back to the garage after a day; I spun the shaft a couple more times as described above. Interestingly, the shaft was much easier to spin. After half a dozen rotations I started to feel it become harder to turn so I stopped. Could be because its heating up, could be because I had run out of assembly lube between the two surfaces. I removed the shaft by rotating the engine on the stand so it pointed down and then, using the same rotating technique as described above, I started to spin the shaft with the wrench. I took the hammer-blunt of a bearing press kit and lighting tapped the opposite end of the shaft through the freeze plug hole on the trans side of the block. The shaft came out nice and easy. I inspected the shaft and it still looked great. I inspected the bearing and it too looked great. Both of the bearings still had their respective oil holes lined up and neither had budged at all. However, my theory about the lube running out was correct. No oil pump means no oil supply; lube is just for initial timing rotations and very first start up.
I cleaned the inside surface off both inner and outer bearings with a super clean non-lint cloth; as too their respective surfaces on the intermediate shaft. I did this for awhile and made sure that all surfaces were as spot free as possible. Thinking on it, any dirt that may have gotten in the lube while I was assembling it the first time is not only very bad but would make it hard to turn. I cleaned all my working surfaces and double cleaned around the entrance to the shaft hole (yeah I said it.) A pair of new gloves and away I went with the assembly lube. I applied triple the amount I applied the first time on all four surfaces. I managed to get the shaft back in (same method as described above) with much less effort than the first time. After it was in, it was significantly easier to turn than before, not as easy as before the bearing replacement but they are new bearings; not worn ones. At this point, I am satisfied that this is alright. After researching its clear the two surfaces will mate upon break-in and the after priming the oil pump/system it will receive lubrication immediately upon startup.
I completed the remainder of the intermediate shaft install by replacing the seal and o-ring of the flange (as well as the stretch bolts) and then TTY.
Hope this helps!!