I want to Thank everybody who helped me through the rebuild of Shurley ( slowly but SHURELY ) I got  to fire the CT3 off today. 2/nd kick it fired off. I had to adjust the idle but it was a fantastic feeling to know that all went well ( so far-haha). There are a couple of small issues When I put it in gear it jumped a little and died. I adjusted the cable and I can feel the clutch but it still lunged and died. I rolled it down the driveway and put it in gear and what a good engine. The second is the petcock is a down pipe and I need a 90 . The bottom screws off and I am not sure where to buy the piece. Any ideas? It is an aftermarket- Enclosed is a before and after. Remember she is turning 50 so don't laugh at her wrinkles.                 

Clutch plates stuck together seems to be a common problem on older bikes when they sit a little bit. I had the same problem. I tightened the clutch cable as much as I could with the cable adjuster. Then I just rode it around in first gear and cranked the throttle a bit while holding the brakes on. After a few minutes it popped loose. Fine now.

Sorry I didn't put on the post that it is a new clutch. I can feel it and adjusted the cable. I adjusted the push rod before start up ( ran it in till it touched then backed off 1/2 turn ). I may have to burn it in maybe. I cleaned the plates and they were in good condition and did not put the rubber rings back in. With the clutch springs not fully tightened down I could see it working before I buttoned it up.

I guess you did tighten the screws fully before buttoning the cover up. Hard to say why its hanging on. Is the clutch hub free to turn without plates fitted. If not the problem is there & we'll start again. Have you had the motor fully apart. Oil level about right. have seen them full to the top so clutch is paddling through the oil.

I tightened the screws by hand and then 1 tap tight each with an extractor. I wanted to flush the engine again so I am now draining to start with fresh oil. The clutch was free and both rods and ball are there. I am not sure if I should pull the cover before i add oil again. It might be beneficial and I can always make another gasket. As far as the motor goes. I did a top end and new clutch with fresh bearings and seals. I did not break the crank apart as the bearing looked good when I was replacing the seals. The motor rotates with out a problem. It is very strong. I might add oil and try to drive it a bit, but no plates, so I need to haul it out th the dirt fields.

The clutch on my CT3 wouldn't disengage after I replaced the friction plates.
I rode it a little in my driveway and went through all the gears and it eventually freed itself and has worked fine since.
Not sure why it acted differently to my CT1s as they all have the same new friction plates.
One difference was that I thoroughly cleaned up the steel plates on the CT3 and maybe that caused the friction plates to stick initially.

I did clean the plates. They were pretty dirty and I knocked off all of the nasty. I think maybe a little driving and see if it improves. If not then pull the cover off and go through everything-1 step at a time. Note I did not replace anything on the internal side adjustment. Threw on a new cable and adjusted.

I only asked if it'd been fully apart because "17 in the clutch has minimum end on clearance for the hub to revolve with clutch disengaged. So having possibly been tightened many times over the years the end clearance can disappear even though it shouldn't It might have had the kick gear replaced behind the basket--doesn't take much. So important to be able to revolve the hub minus plates freely. Not much that can cause clutch to hang on despite very warped plates which is unlikely. In the link the plates are drawn wrong & need a steel in "last" & "no" steel in first if your clutch is this model.
Spacer 17 i was referring to. Sorry for pushing the point & long winded but clutch should be perfect straight away with new plates & lifting properly.
www.partzilla.com/catalog/yamaha/motorcycle/1973/ct3/clutch

Thrust washer can slip down or get mixed up during assembly too...  gets pinched and clutch won't disengage.

Always make sure inner hub spins freely and independently of outer basket after inner nut is tightened and before installing plates.

I think it is time to pull the cover and go through this again. What concerns me is that it was disengaging before I tightened the tension springs. I figured the leverage provided by the handle was what would overcome the tension from the tightened springs. Question. How often do we replace #18 thrust plate --#3 thrust washer-- and #2 flat bearing . I used all of these parts again and did not think much of it at the time.