Good news is that after rebuilding my engine, running great.

Bad news is that when I went to attempt the road test there was an issue with the clutch which I had replaced with an exedy (OEM for Honda). The original flywheel was checked for flatness and skim cut. Aligned and installed without any issues.
Can move through all the gears without issue when the engine is off.

The problem is that I cannot put into any gear, with the clutch pedal in, when the engine is running. Starts to shudder if I start to try to gently force in any of the gears. It almost seems that the release bearing is not engaging far enough even though the pedal is moving the release fork a good couple of inches.

Any ideas on what I may have done wrong on the install? If necessary, I will remove transmission but want to see if there are any other options first.

 

Was the clutch system opened ? If so, it's possible there is still air in the system.

 

Good point, the hydraulic system was opened as I replaced the main and slave cylinders. I did bleed it down but maybe it wasn't done well enough. Will try again. Any tips for making sure system is 100% completely free of air?

 

With the reservoir cap off, have someone rapidly pump the clutch pedal as you squeeze up and down the rubber reservoir hose. I've seen pesky air bubble pockets get stuck in that area and you may see bubbles rise up through the reservoir.

You may also need to adjust clutch free play. You only need about an inch of clutch free play at the pedal.

Bleed it through one more time.