Responses from eldarado

Simaudio I3 or I5...
IMO, depends on what type of music you listen to. If rock is heavy in your rotation then go with the I-3 if not, the I-5 is best choice. Good luck. 
If you lost your stereo system would you still ???
I would go with a headphones. You can get a pretty decent headphone setup for $500. I didn't say good but, descent. I spent somewhere between $500 and $1k on my headphone setup when the main rig had to go because of the arrival of twin boys.I like... 
Help chossing a good speaker. $ 3-5 K
Have you gone to see John Fort and listened to any of the Vandersteen line here in Dallas? His store is nothing special but, he is the best audio dealer here in D/FW, IMHO.Crystal Clear Audio carried Totem the last time I was in there (been a long... 
Rogue M-120 and M-150
I have a buddy that had 120's upgraded to the 150's and there is a very noteable improvement. Pretty much an improvement in all aspects. Well worth the extra money for the 150's, IMHO. He is driving Vandy 2ce Sig with them. 
Quatro and 2 Ce Sig II ?
What is your question? 
what is the weakest link in my audio chain
This is my opinion.Replace first (top to bottom)SubSpeakersCD/DVDCablesampI don't know anything about the AV8 so can't comment on it.Good luck 
Starting over
I went the heaphone route when I had to get rid of the main rig due to twin boys arriving. Got the Senn 650's and a Mier Audio Corda Aria amp w/ the built in USB DAC. I have to say I have been pretty happy with the it so far. May try going with a ... 
Record is noisier after cleaning:
Not to hyjack the thread but, Freon (R-12) has been banned from being produced in USA for well over a decade. R-134a, the propellant called out on the spec sheet, was around before 1995. Both used in refrigeration and as a propellant in spray cans... 
I need help with the audio side
What is your budget? This will help everyone here give more useful suggestions.I currently have no budget so, I am jealous of everyone that has one. No matter how big or small. 
Help me spend $5,000 on a 5.1 speaker system
You might look at the Paradigm line. All of their speakers are pretty efficent and that will be a good thing with the Pioneer receiver. The Studio Line should fit within your budget new. 
Need Some Help Choosing an Integrated Amp
Pathos Logo might be a really nice match with your current speakers. 
Sim I3, I5 or Music Fidelity A3.5, 5 with Dyn 140
Of the Sim units go with the I3 over the I5 for rock.Never heard the 3.5.The A5 has plenty of power and would probably be my choice of the four you listed for rock. 
2-3K, Integrated or Seperates
I would go the integrated route. There are a lot of really good units out there in the $2-3k range. So many that it may hard to make a decision. Good luck. 
How can I improve my system
I am on board with Shad and Tvad. Before you go chasing your tail by replacing components, look at your room. Do you have any type of treatments currently? Have you tried changing the placement of the speakers? IMO, the room is the most important ... 
BookShelf Speakers Sound Muddy HELP
I would suggest bringing them out into the room some more.