Cylinder Bore/Length/Volume? Air/Fuel Ratio?

Remember the Prius is Atkinson Cycle not Otto.
I believe this delays the closing of the intake valve to reduce the volume of fuel/air during the combustion cycle. This may come into play for some of your calculations. Or not.
J

 

Toyota's Technical Information Service is described in detail here.

For a small subscription fee, you get access to the entire technical library. In particular, there is a volume there called the "New Car Features Manual" (the NCF tab, online) that contains all the specifications you are looking for. They may be repeated in the Repair Manual (the RM tab).

In addition, that library has "Quick Technical Guides" on a variety of topics, technical service bulletins, special service and warranty campaigns, and (under a separate Technical Library tab at the top) course materials used in "University of Toyota" technician training courses.

You might find a lot of that, beyond just the bore and stroke numbers, useful in your project.

 

The cylinder bore and stroke of the two main engine families used in Prius cars are, for the 1NZ-FXE (2001–2009 and Prius c ), 75.0 mm × 84.7 mm, and for the 2ZR-FXE (2010–present), 80.5 mm × 88.3 mm.

As @ChapmanF kindly mentioned, the New Car Features book is a good source, and the other materials on Toyota’s TIS make it well worth the modest cost. In particular, see the Engines chapter of the Technician Handbook for the Hybrid Systems (T071) course, and the Advanced Emissions and Drivability Diagnosis (T972) course, which has a good explanation of air/fuel ratio and its effects on emissions.

I’ve previously suggested some books on hybrid vehicles; in particular, the Hayes and Goodarzi book takes a much more quantitative approach than you’d find in materials prepared for technicians, and they may have already worked out some of whatever you’re analyzing. @bwilson4web kindly reviewed some SAE technical papers from authors at Toyota; there were similar papers about the engines and drivetrains of earlier Prius cars. Oak Ridge National Laboratory did teardowns of the hybrid systems in the 2004 and 2010 models.

If your focus is the engine itself, see Garrett’s The Motor Vehicle, Bosch’s Gasoline Engine Management: Systems and Components (or the standard Bosch Automotive Handbook ); SAE’s Internal Combustion Engine Handbook; and Hoag and Dondlinger’s Vehicular Engine Design.

 

Pseudo Atkinson Cycle.
Yes it does tricky stuff by varying the intake valve.
That is why it can burn regular gas, but it has a High Compression Ratio, on paper.

I've always wondered if it does not lose power with altitude, to a point, compared to a normal engine.
Does it maintain an effective compression ratio as the altitude increases?

 

I think it has a high expansion ratio, in contrast to a low compression ratio. It would be Otto cycle if they were the same.

I'm not sure you need anything beyond a low compression and high expansion ratio to be a bona fide Atkinson cycle engine. Atkinson's original design accomplished that by a different mechanical arrangement, but I'm not sure that's the part that matters.