Hi Scotty! I love your show BTW!
I have a 2008 VW Rabbit with 96K miles on it and the CEL will start flashing if I idle for about 5 - 10 mins and will be solid if I rev it up to over 900 RPM. I get misfire codes in cyl 1, 2 and 5 as well as a random cyl misfire. I proceeded to replace the coils, plugs were replaced like 20K miles ago, didnt fix the problem so I took it into my local shop for further testing. They took the intake manifold off and the valve cover off and had a look at the valves no problem, told me there was no problem with the vacuum seal or fuel pressure also said the electrical ignition was ok. Said the misfire was happening primarily in cyl 5. Then the shop replaced the crank and camshaft position sensor and did a fuel injector cleaning and reset the ECU. They TOLD me it was fine but as soon as I got the car back, the CEL came on and started flashing. The cat converter busted around the same time the CEL light started flashing the first time. I replaced that since it was very loud. There seems to still be some rattling still but it doesnt seem like the timing chain, more of something either in the clutch/transmission or the exhaust (it comes from underneath the drivers seat) ... Im not sure what else to do at this point... my local shop offered to put in a few free hours for me since I paid an arm and a leg for my car to have the same problem.

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That rattling under the drivers seat also only happens at idle or very low RPM intermittently, gets worse when i push the clutch in and when i lug the engine a bit a low revs which makes me think its a transmission problem. But everything runs OK if i just heel toe it in NYC traffic, burn a little more gas to keep the revs up :P