Clutch or Synchronizing Gears

I finally got to do a little driveway test after the engine rebuild.  The good news is the engine runs great.  Bad news is that I am having some issues with getting it into second gear when in motion.  I replaced clutch and pressure plate.  I used the appropriate bolts with shoulders to fasten the pressure plate to fly wheel with 14lbs.  I still need to do the final adjustment on the clutch cable as I replaced the clutch bellcrank and cable.  The throwout bearing doesn't seem further than an 1/8 away from fingers.  But I really have to depress the clutch petal pretty hard to get separation from the flywheel.  The issue I am having is when I go from first to second I get grinding on the gears.  It is like the clutch is spinning to fast to engage the transmission shaft.  If I keep my foot on the clutch for 4-5 seconds the rpms finally slow down enough to were I can put it into second when the jeep is moving.  Is/are my problems:

1).  Pressure plate is too tight to flywheel or clutch is not centered on flywheel.  It looks a little wobbly in video.

I agree,,,, but looking at the space between throw out brg and pressure plate Im guessing you have at least 2 to 3 in of free pedel.  adj and try again.  It does seam that almost every manual tran has a sweet spot they like, find it and go...

I just did mine. Like others have said, adjust your clutch cable or clutch rod (if adjustable) to 1" pedal and close to 1/8" space on throwout bearing. Also make sure your clutch crossover tube has short end on the chassis side. 

I had to replace the clutch cable to the old one.  The new one I ordered was too long.  But finally got it to shift into second and third.  Thanks for the tip on pausing for a second before going into second or third.  

And the clutch would function properly?  Installing the clutch backwards wouldn’t allow the clutch to sit flat on the flywheel.  And why would the noise be intermittent?

"I am thinking maybe the clutch is not centered and the off center is making it shimmy."

I am not sure on the idle RPM.  But if the throw out bearing was touching, wouldn't it spin?  I did have to manipulate the engine a little to get the bellhousing and engine studs to line up.  It was off an 1/8 to 1/4 of an inch, so I am thinking the clutch is off an 1/8 to 1/4.  I think I am going to just pull the engine again and replace the pilot bushing and use the clutch centering tool this time.  it looks like the transmission main drive has a slight wobble.  It is tough to tell  with the pressure plate moving around, it could just be an optical illusion.  

I guess there is something that always needs to be done.  I finally was test driving over the last few days and the engine was running great.  It started to sputter and lose power when I stepped on the pedal.  I was certain it was a fuel problem, either plugged jet or pump.  Spent half the day trouble shooting.  Nope, it was a bad condenser which was brand new.  I put the old one in and it ran great.  I thank the forum.  It is an encyclopedia of information.

If the clutch is off 1/4-1/8”, I don’t think you can put the transmission and engine together. Input shaft wouldn’t go into pilot bushing

Turns out the pilot bushing was severely worn out or someone put the wrong one in.  The main drive had probably a 1/4 inch of play to the bushing, maybe more.  I swapped out for a new bushing and the noise and vibration stopped.  Luckily I saw an old post about bread and a wooden dowel to remove the bushing.  No back to trying to tackle the regulator issue.