Need help diagnosing my 348 rattle and possible clutch

Ok...I have thoroughly read this archives, here is my dilemma and would like some help on a possible course of action.

When the car starts up, there is a slight rattle in the back, it usually goes away after about 5-10 seconds.
Twice (2 weeks ago and 700 miles ago) the car stalled twice while breaking at a light, has not done it since
The check engine 1-4 light comes on intermittenly often and will stay on at times for about 15 min-20 min at the most, it usually goes off when i am at sustained speeds of around 80 on the highway
The check engine 5-8 light has come on once or twice, about 600 or 700 miles ago also
When the car is in neutral, i can feel a lot more vibration on the pedal then when the clutch is depressed..is this normal? It is nothing loud or obnoxious but I can definitely tell the difference between when the clutch is depressed and when it just sitting in netrual...it sounds like something could by grinding in the back (not sure if that is normal because i have never owned one of these cars before)
Hot starts, sometimes it takes a little bit longer to turn over...not much, but i was wonder if this is what people refer to when the talk about hot start problems

WHEW....OK...From what i have read it sounds like 2 things (and if there is possibly more please chime in, im just a rookie who does a lot of reading on this site)

1) Possible cat going bad? I have read that the ceramic breaks up and will rattle around in there. Even if this is not the problem, I will probably replace the cats anyway with the hyperflows just for sheer piece of mind...It seems like you pretty much reduce your chance of engine fire from about 20% to .01% just by getting rid of those cats...
2)Clutch on its way out? Not sure what to do about this...I am on a limited budget but I would rather nip the problem at the start then shell out big dinero for something that was left unattended..

I have to get a major service done also so all comments or suggestions on how to get this done the cheapest but still the RIGHT way please chime in.. Im not to mechanically inclined, although my neighbor is very...but i am all about going to independent mechanic, finding parts myself, and cutting some of the costs that way...
Any help would be greatly appreciated...one more question..I am assuming I should just leave the car in the garage and not drive it, correct?