manifold vaccum for vaccum advance ?'s

ok, i'm taking it to a shop then because i dont know how in the hell this engine could possibly have a miss?? Brnad new distributer curved and phased. Brand new cap and rotor brass contacts. Plug wires are fiarly new borg warner select 7mm's, plugs are fairly new ngk v-powers and i have triple checked my firing order it is correct.
And when you drive it there is no miss at all, i can go all the way to 6000rpm and it dont miss a beat???
But while its at an idle, you can hear the thud thud thud out the exhaust, i'm really starting to think this broken intake manifold stud has aot to do with whatever the hell is going on with this thing.
I will set up an appointment with my buddys shop to have a compression test and a leak down test done. And i will go from there, depending if everything checks out good? then what could be causing this engine to smoke when backing off the gas? bad valve seals or valve guides? or both? I just read that the valve guides and the valve seals can be replcaed with the heads still on the engine. I guess i will need to get a second opinion on this.
Maybe i should get the broken bolt out, then get a new intake manifold gasket, get the broken stud drilled out put a new bolt in it, bolt the intake back down and if i still have this thudding out the exhaust issue and smoke coming out the exhaust when backing off the gas i will have to think its ehter valve guides or valve seals then, correct?