2001 A4 Quattro 2.8. I bought the car almost 3 weeks ago and up until yesterday it has run very well (the only work I've done on it so far has been replacing the exhaust flex pipe and the air intake temp sensor which did not fix my climate control problem). It has run and driven very smoothly and brought me home from work Friday with no issues at all; or did it start just a little slower than normal before my 20 minute drive home? About 30 minutes later I started the car and it ran very rough - sputtering and very low idle and a flashing CEL. Obviously I was missing on at least one cylinder (and 'obviously' meant it was probably multiple cylinders).

So I plugged in my OBDII scanner (I don't have a VAG scanner) and here is what I came up with on the last scan (when I tried unplugging the MAF):

p0170 - this one has actually been there since I bought the car.
p0341
p0300
p0301
p0303
p0302
p0600 - this one only showed up for a moment then went away
p0306

I know this means I have a misfire across both sides of the engine and, judging from how rough it's running, I'm guessing it's actually a 'no-fire' on some of those cylinders if not all. This last time I started the car it had a 'rattle' that sounds a LOT like I'm running an old diesel engine and the idle had dropped off to only a couple hundred RPM. And then it died altogether and it doesn't want to start at all now. I searched and I couldn't find anything that was quite the same as my situation. I'm ok at troubleshooting and turning wrenches but I'm not even an average Shade Tree Mechanic, Sooo...

I apologize if it turns out this is a common question/problem/fix but I really need someone to walk me through the troubleshooting. Thanks in advance!

 

*Update*

OK... I called the shop (not Audi - just reputable local guy that was willing to come over and take a look). He got it running but believes the noise is serious internal damage such as bent or broken rod or something like that. On the bright side, he did not make my day worse by charging me for the house call. I can get the car into my FIL's shop and tinker with it but I need a little input.
Is it worth it? If I'm going to figure out what's broke inside, where do I start, what do I look for, and what should I expect?

Part of what I'm wondering: The rattling noise - what could cause it, simplest to most difficult and where would I start looking, least invasive to most. What can I work on without pulling the engine? How deep can I get into this without having a Doctorate in Audi Sciences?

I really need some help here guys. I'm not independently wealthy buy I can afford to buy parts. Let's just say time is at a premium but I still have a lot more of that than money. I'm also not afraid to tear into the engine a little if there's a reasonable amount of hope that I might be able to fix the problem (without getting in WAY over my head-I can turn a wrench, even a torque wrench, and I have access to a lift and shop space).

Is it worth my time and money or should I walk away and be glad I didn't throw good money after bad?