I went thru the exact same process a couple of years ago. I'm no expert so I welcome corrections if corrections are due. First I'll say "KR500" is pretty close on costs of new stuff. As for the value of the existing dual quad set-up, value depends on exactly what you have. If the intake and carbs are correct for 67 GT500 I think the value will be greater than over-the-counter parts or parts off a non-Shelby application. Best situation is to have the correct C7AZ intake and matching pair of C3AF-9510-BK/BJ carbs. Many times the carbs will look correct but you find 9510-U carbs which are service replacements. I thought I had a correct setup but later found the air cleaner was a repro while carbs and intake were good.
As for 68 KR parts:
Carb will be $1000 up for a rebuildable core. Restored $1500 and up, but varies with your configuration (4spd vs auto)
Intake will be $400 and up. If you want to be date-code correct you'll need to allow some time to find the right one and be willing to pay when you find it.
Air filter, snorkel, s-tube and heat shield, $4000 for original, $2500 for repop.
Allow $300-400 for misc. specific parts for PVC setup, vacuum fittings, etc.
I don't know costs on thermactor set-up since I haven't replaced mine. Depending on your current setup you may need to replace some pulleys. There also might be some work where the thermactor tubes connect to the exhaust manifolds.
As Bob said, the plenum had to be modified for the 2x4 air cleaner to fit under the hood so include $200-$250 for reproduction plenum.
After all the above, throw in $1000 for shipping, belts, hoses, paint, cleaners, etc.
None of this includes labor or other incorrect parts you find along the way.
If you purchase the car don't think you will be shunned here for having none correct parts on your car. If you get it for the right price, drive and enjoy. Our KR successfully ran like a scalded dog 40 years set-up like yours. I only decided to put it back to a single carb when the 2x4's need rebuilding/restoring.
Ted