Sounds like a great find! Unfortunately, it's very difficult to confirm a true Z24 car without the build sheet. You say this car has the Z24 Hood, SS 427 Dash Emblem, and front and rear SS 427 Emblems, so it's probably a good bet that it is the real deal. If this was a Canadian built car, it would actually indicate "Z24" on the Cowl Tag, so it might be worth checking if you haven't already. Those of us with U.S. built cars are not that fortunate!
As far as the missing Gills, if they were ever there, there should be three rows of three vertical holes drilled in each front fender. Check the inside of the fenders (can be seen with the doors open) to see if there are any burrs behind the holes. If the holes appear to be clean and free of burrs, they were likely put there by the factory, and not added later. All RPO Z24 cars had the Gills. You say the 12 Bolt is missing, but you don't indicate what's under there. All Z24 cars would have the 12 Bolt with either the F40 or F41 suspension.
Your Engine suffix seem a little confusing to me. TO413IVR? T=Tonowanda, 04=April, 13=13th day, IVR? To begin with, this appears to be one character too long. Any chance you misread this? The last two letters of a `68 L36 suffix with a 4-speed would be either IJ or IS (ID for an L72). MIght want to clean this up enough to read it again. The first part of your VIN will also tell you where the car was built, and may give you a clue as to where to start looking for your build sheet. Different factories put them in different locations, although this was never cast in stone. St. Louis built `68 full size cars reportedly never included build sheets, so this is sometimes hit or miss. Good luck with that.
This car as you describe it is also a Z03 (SuperSport) optioned car with the Bucket Seats and U41 gauge Package, so at the very least, it's an SS with a 427 if not a Z24 SS427, which was a stand alone model in `68.
As far as the worth of this car? In my opinion, if you can drive this car home for $10K, this is a very good deal! Good luck. Hope this helps.
`68 SS 427 L72, 4-Speed Z24/Z03
`73 SS 454 El Camino
`97 SS Camaro Convertible