Yes , this seems to agree with your syptoms.
If you feel all else is ok , i would check for 180 degrees out of time.?
Check and follow the manual procedures exactly ., its a common mistake to go 180 out without knowing it . Dont know if this condition would allow one cyl. only to fire .?

 

how could it be 180 out if the marks on pinion, cam and breather are aligned properly?

 

A common mistake to have the cam 180 out?

Seriously....

The cam cannot be out of timing by 180 degrees.

It rotates at half the crank speed.

The marks will line up every other crank revolution.

OP:

I don`t think you are adjusting the pushrods properly.

 

Thanks for all the advice. Believe me, I've tried everything that's been suggested. Here's where I'm at now-I've readjusted the push rods three times by turning the rear wheel in fifth gear until the lifters for that cylinder were at the lowest point. Push rods threads are 24 per inch, so I adjusted the rods out 2.5 turns. I let each cylinder bleed down for 30 minutes before adjusting the next one. I removed the nose cone again and checked the cam alignment. Dot on the left lines up with the straight mark on the black plastic oil gear. Dot on the bottom of the cam aligns with the straight mark on the pinion shaft. I've checked this alignment three times now. It looks just like the service manual shows. I removed both rocker boxes today and turned the motor over with the spark plugs removed. Everything seems to be working in sync. Push rods are going up and down, rockers are moving, pistons going up and down. No grinding noises, nothing banging in to anything. Did a compression check this morning and front cylinder is at 200 psi and rear cylinder has practically no compression. If I put my thumb over spark plug hole of rear cylinder, I feel just a slight blowback, small amount of pressure, not enough to register on the compression guage. Rockers, pushrods, and piston for rear cylinder all seem to be moving correctly. We rode to Biloxi, Miss and back last Sunday-400 mile round trip, and on the way home I noticed a loud tapping at around 70 miles per hour. It was intermittent at first, but the last 30 miles it was pretty constant. Not a grinding noise, just loud tap. I thought it was one of the lifters, so I replaced all four, but that didn't fix it. I thought about just biting the bullet and putting a new engine in it. Called every Harley dealer in a 300 miles radius and you can't find a "new' evo engine. Also, Harley Davidson has discontinued their remanufacture program for evos. It's strictly for twin cams now. My next thought is to pull the head and jug on the rear cylinder tomorrow and check to see if I could have a busted valve seat or a broken piston ring. Anything that would cause a loss of compression. I've got no choice but to fix this motor, can't buy another one. The bike is in great shape except for this compression problem on the rear cylinder. I know this is a long post, but thanks for the advice so far and please let me know if there's something that I'm missing.

 

http://dallas.craigslist.org/dal/mpo/4657208483.html

 

If you are seeing the valves closed on the compression stroke, and the cylinder builds no compression, you're gonna have to pull that head. I'm betting on an obvious cause once you do that.

 

Remove rear pushrods and put air in the cylinder, then you'll know for sure where the compression leak is before you remove head.

It could even be a blown head gasket.

 

FWIW I played hell adjusting some screaming eagle pushrods one time.
I had to do it about 10 times before it worked right.
I have no idea what I was doing wrong. I was following directions but they just wouldn't be right.

 

did you try a compression test on the rear with the pushrods out? that would rule out the valves and seats if it shows good then...

 

If the pushrods are removed, a leak down check would be the thing to do, not a compression test.