Do you think the "girgling" noises your hearing are due to exhaust leaks? I can't imagine what Pep Boys is including in the $400 + exhaust manifold gasket replacement. This job shouldn't cost any where near that amount of money.
Generally, when I hear someone describe a "girgling" noise, I think about the cooling system and possible air pockets, which if accurate in your case may also relate to your temp gauge rising on your trip. Have you checked the coolant level?
Your knock sensor job is relatively easy and most likely can be done by you at home.
As for the cel on for years in your in-laws cars, this can be very dangerous to the vehicle for 2 main reasons... 1) if the underlying problem is an important component for the engine or transmission management systems, the computer will refer to certain default settings, which may be ok on the short term, but cause much bigger problems on the long term if ignored. 2) If the light is on and something more serious develops then you have no warning at all because your used to seeing this light on.
For more information on your check engine light etc feel free to review my website at http://www.5starservicenter.com
Good Luck!
Rich