Motorcycle Repair: CB1100 having a hard time starting, valve clearances, rattling sound

Question
Hello,
Just bought a 83 CB1100.  The original owner had to put on a new head.  The question that I have is, the timing looks fine and the lash between cams and valves are within tolerance but, the bike has a really hard time starting and is making a really bad rattling sound (sounds like a pair of drum stick tapping on a tin can).  As you rev the bike, the sound becomes loader.  I did see that it also has an aftermarket CCT.  I have tried adjusting it and nothing, the bike will almost stall but, the noise is still there.  Someone told me to pull the heads and check for a bent valve.  Have done this and saw nothing.  Also was told that if the timing is out by 1 degree, the bike will start but, the lash will cause the rattle.  So, I reseated the cams according to the service manual and still nothing.  I was told that when the owner installed the head, cylinder 1 and 3 were up and 2 and 4 were down.  I was looking at another motor and saw cylinder 1 and 4 up during TDC.  Could the timing be 180 degrees out and if so, would the bike start.  Which cylinders should be up during TDC?

Thanks

Answer
It better be 1 and 4, otherwise someone has done something really strange with your crank!  Both cylinders fire at the same time, one is a 'wasted spark' the other one is on compression and powers.  I would check the valve clearances, since they will tap loudly if the clearances are wrong.  Is the noise coming from the head area or lower down?  Let me know,  Jan