I have built two bottle rockets with clear fins, learning from the first one such that the second one is a better overall design. My first comment is make sure you use Lexan fins; other plastics will snap. Second, there are very few glues that will stick to the bottle reliably, so I do not depend on the bottle holding anything. Effectively, I build a rocket inside the bottle with the fins sticking out.
First, I empty the bottle of any contents and cut off a hole in the bottom about 4 inches in diameter. I then wash the inside (if the bottle came with popcorn, it will be full of grease) and let dry.
For attaching the fins, I use two PML 54mm-6 inch centering rings. The rings are cut to the same diameter as the inside of the aft end of the bottle. These rings end up being sliced and having pins because they are bigger than the aft hole of the bottle so they will get reassembled inside the rocket when they are finally installed. Each fin is a mirror image of the other and have three 1/8 dados in them and holes. The dados are where the three fins will end up, and the holes allow tabs in the fin to lock the fins in place. The inside of the centering ring is notched where at each of the dados so that the alignment U-channel will fit over it. Additionally, there are 3 more holes. On the upper centering ring, T-nuts (10-24) are installed facing away from the fins.
Next I take a 54mm tube and glue 3 five inch pieces of 1/8 brass U-channel to one end, starting about 3/4 of an inch away from the end. Eventually, these will be used to align the fin and the centering rings so these need to be evenly spaced around and parallel to the tube. Also glue a recovery strap to the inside tube.
I then temporarily put the rings on the 54mm tube and use my longest 10-24 screws to space the two centering rings apart. The fins are cut so that they fit between the centering rings with tabs where the holes are. Make sure you can still have the screws in and the centering rings far enough to allow the tabs to come out. Otherwise you will not be able to put the fins in once everything is inside the rocket. My fins are elliptical outside the bottle but you can make any shape you want. After making sure the fins fit, remove the fins and centering rings from the 54mm tube. Reassemble the centering rings inside the bottle, making sure everything is oriented correctly.
With the centering rings in the rocket, I put the tube inside the rocket with the U-channel on the aft end and it sticking out about 1/4 inch on the forward end. Using the centering rings to align the tube, I use a clear hockey tape (or any other tape that epoxy does not stick to) to seal the small space between the 54mm tube and the top of the bottle. With the bottle pointing down, I then fill the space between the tube and the bottle with about 1 inch of liquid epoxy (such as West System) which I squirt through a piece of airline tubing inserted into the rocket (the tubing avoids making a mess). The epoxy conforms to the shape of the neck so the bottle if firmly joined to the tube even if the epoxy does not stick to the plastic. When the epoxy is cured, I remove the hockey tape.
I then glue the aft centering ring to the 54mm tube as far aft as it will go. Once cured, I do put a little bit of Gorilla glue between the centering ring and the bottom of the bottle. The Gorilla glue will expand enough to cover the space and does stick to the plastic (but the 54mm tube takes all of the forces in this design). Using the outside ends of the dado as guides, I carefully cut three slots in the bottle where the fins will go. The three 10-24 screws are put through the aft centering ring and screwed into the T-nuts in the forward centering ring. The forward ring is slid forward and the three fins are put in place. The screws are tightened and the tabs hold the fins in place. This allows the fins to be replaced if one is broken (but Lexan will not break!).
The next, two holes are drilled through the bottle, one into each centering rings. These will be used to mount the rail buttons. Initially, the hole is big enough allow the rail button to be threaded into the wood. Then the hole in the bottle is drilled large enough to enable a spacer to fit between the centering ring and the button. This way, you rely on the centering ring to hold the rail button in place and not the bottle. Screw the rail buttons and spacers into the centering ring. Do not use glue in case you ever have to remove a fin.
Add your motor retention. I prefer a 54mm Aeropack as it will keep all forces on the 54mm tube and not on anything else.
The nosecone is simply a 54mm piston with an eyebolt facing inside the piston. A few washers and the plastic bottletop are put on the outside of the piston. I do not allow the bottletop to snap onto the bottle. The piston provides enough friction to prevent it from coming off so the bottlecap rests on the end of the 54mm tube, just looking like it is fully on the bottle.
You will need to add weight to the "nosecone" and additional washers on the eyebolt work fine.
This is not your average build-in-a-weekend and does require some special tools to get the dados right (I use a radial saw and it's kerf is the same size as the fins) this could be gotten around if you did not have the tools.
Mine bottles have flown many times. One kept the original beer labels and is used in general launches. The other I peeled off the original label and installed a vinyl enlargement of a local brewery's root beer. I use this at launches aimed at kids (i.e. Cub Scouts).
One final note. I live in VT and we fly all winter long. But I do not fly the beer bottle rockets when it is cold. The plastic for the bottle gets brittle below about 40 degrees.