I'm afraid I don't even begin to qualify as an "expert" but I know enough to be somewhat skeptical of your mechanics. I can see them not being able to adjust your mixture enough, but I have a hard time understanding how they would send you off to the emissions test w/ your car pumping out that many HCI. There are some boneheads out there masquerading as mechanics, and there are plenty of mechanics out there who are hiring untrained kids to do jobs THEY should be doing.
I agree with Oscar. Take it home. And take your time. Don't trust the first mechanic who tells you he's going to have to replace your engine. Don't rush into something like this.
As someone who is generally able to take one thing off and bolt something just like it back on - but often lacks diagnostic skills - I am finding the internet to be quite helpful. Pay close attention to everything that you are noticing with your engine performance (or lack thereof), write it down in list form, and then type it in to google. You will likely see a fairly short list of possibilities start emerging. Also, since you've been told you have two dead cylinders google "dead cylinder" and "car," read what the symptoms are, and then see if your symptoms match. Big Richard gave you another candidate in suggesting a blown head gasket. Google it and find out what would happen if you have a blown head gasket.
Heck, at least when you take it back (to another mechanic for a second opinion), at least your reading would help you sound like someone who has a clue, rather than some sucker waiting to get screwed.
Sorry I can't be of more help than a few general suggestions. I sure hope it's just something like a bad head gasket, or that the shop screwed up the adjustment so bad it's off the charts, or something like that. Keep us posted what you learn.
Mike
Here is an example of a useful, informative article I found by entering "dead cylinder" (with the quotes) in google:
http://autos.yahoo.com/maintain/repairqa/engine/ques053_1.html