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Ive got a 1979 kz650 b3 that im restoring. I got it running but it was only running on cylinders 1 and 4. First i thought it was the coils because i just rejetted the carbs and i know 2 and 3 are getting gas. I ran the bike with the carb boots off. I put my hand over the intake of the carbs. 1 and 4 killed the bike when i put my hand over the intake. On cylinder 2 and 3 i felt vacuum and when i took my hand off there was gas on my hand. I noticed there was no spark on 2 and 3 so i replaced the coils and now i have strong spark on all cylinders. Then i took the plugs off and put my thumb over the holes. On cylinder 1 and 4 the compression pushed my thumb right off and on 2 and 3 i didnt feel anything. Also the plugs on 1 and 4 looked good and on 2 and 3 they looked brand new and they were wet with oil. Please help. 

It's interesting that it's 2 and 3 that have no compression.  Have you checked cam timing?  What about valve clearance?  Do you have a service manual?

I hav not checked the timing yet. The valve clearances were set by me back in 2017. But after that i barely rode it. Last time i rode it was in 2018. And after i set the clearances it ran great. Its just been sitting ever since because of a carb issue. But now i started working on it again got the carbs all cleaned and rejetted with original size jets. now this compression issue. 

I have a service manual on order because i lost mine. Should be here in a couple days. 

Also i set the timing when i put the electronic ignition in years ago. 

I just recieved my new service manual so im gonna check the timing and valve clearances when i get home from work tonight. I also might look in the cylinders with an endoscope first. 

If you have a compression gauge it would be helpful to quantify your compression in all cylinders.  The manual will explain how to do it.

I do have a compression tester but it doesnt have the right tip. Either it didnt come with it or it was lost at some point because im pretty sure these threads are a very common spark plug thread. Im pretty sure my truck uses the same threads. 

When you check your timing you can put the timing marker on "T" for 2/3 and check to see if the pistons are at top dead center.

I'm not sure of the relevance regarding timing given that a compression test is purely mechanical and carried out with all the spark plugs removed ? 
I suspect after such a long lay-up (and with the plugs being oiled) the the rings are stuck. Perhaps a good soaking with WD40 or similar overnight (don't forget to spin it over with the plugs out to clear the excess) may release the rings and recover the compression loss.

So last night i took the valve cover off and rotated the engine with the plugs in and i could hear air escaping through the valves. So my next step is to remove the head and do a complete rebuild on the head. Also the head gasket is leaking a little on the side of the engine by cylinder 4 so that has to be replaced anyways. The bike has 44000 miles on it so i think this is something that needs to be done in order to insure a problem free future for the bike. Ill also look at the rings when i take the head off. 

I will try the wd 40 trick when i get home tonight just to be sure