I am going to enjoy this thread. My first car was a '65 Malibu with a lot of road rash. When Revell first brought this kit out, I had wished that they did it as a non Z-16, but we have what we have. The contour of the rear quarter windows kind of bugged me, so I built a phantom Z-16 convertible out of mine.

Do yourself a favor, and buy a Model Car Garage '65 Chevelle Photoetch Ser. It will give you the emblems to do the car you wish to do. The detail work you are putting into your build will be enhanced with this kit.
In my stash, I have a R&R Resin '65 Malibu SS 2-Door hardtop, which was not a bad re-pop of the AMT Craftsman Annual Kit, with an opening hood. I may do my Malibu SS 2 Door Hardtop using a Craftsman Built-up that I have. The project is a little ways off, but this is how I plan to do it:
The Craftsman kit body is fantastic, in that the hood has to be opened, and components added. The old cratsman kit also has a correct set of "SS" wheelcovers. The promo style mounting bosses have to be removed from them to work with the wheelbacks.
The absolute best '64-'67 GM "A" chassis in scale is from the AMT '66 Olds 442, and that is the one I am going to use. It has a separate frame and floorboard, as well as all of the underhood components.
The engine will come from the AMT '66 Nova. With the exception of the oil pan with the front sump, if you are going to do a 4-speed car, this is a great powertrain, requiring only a correct rear sump oil pan to work. The air cleaner has to be modified, but a the best unit shapewise is in the JoHan '65 Cadillac. The oval snorkel(s) have to be added. The Revell '64 Impala has a nice 327/300 V8 with a powerglide. The center console has to be modified to adapt the automatic shifter and quadrant. The Revell '64 also has a beautiful set of Goodyear "Power Cushion" tires.
The AMT '65 El Camino had some nice interior parts for the project (Bucket seats and console).
Now I could also go the way you are going, and use the Revell Z-16 kit, and do the mods you are doing to the kit, which is far more cost effective, and satisfying. I may take mine, and do a '65 Malibu 2 Door Hardtop. I'll have to scratchbuild the front bench seat, as well as the side mouldings, which I will pattern from the AMT wagon, and I will use a set of wheelcovers from that kit.
I want to do a set of '65 Chevelles, including an El Camino, Malibu Wagon (AMT Kits), a 300 2 Door Wagon (Jimmy Flintstone Resin), and a 300 2 Door Sedan. I did a phantom '65 Sedan Delivery from an AMT '65 Wagon back in 1997.

What color are you going to paint yours?? I know it is going to be great judging from what I am seeing so far.