Car Not Running Right

[(-CRX GUY-)]

I just replaced my head gasket in my 88 CRX Si, it has 198k miles on it... it runs good for a bit but then after a while it starts to idle funny... after about every 3 sec or so it miss's one fire.... then it goes again, then after 3 more it miss's again... could it be cause by a bad vacum in the intake manifold?? is there a certian way to put the intake manifold on cuz i just bolted it up
thanks
JERRY