With lots of respect to Triple R, I would not overly focus on the baffles at this point; the car WAS running without them before, right? Could be a good later improvement; but I have raced an inline 4 a lot with the 500 cfm version with no baffles and no issues. (But who cares about a race car idling smoothly? LOL)
The puff of smoke/gas vapors sounds like one step below a backfire, and indicates to me that that some of the sparks are waaaay off of time (especially with the stock cam, etc.). The ignition could be crossfiring under the distributor cap, or misfiring the spark for a number of reasons.
When you say you checked the timing 3 times, is that with the car not firing, or before the issues showed up? What kind of timing test do you use?