Run the algorithms by hand
Division, Euclid, extended Euclid, fast exponentiation. Each with its trace, so the method transfers to paper.
Everything follows from one theorem about division with remainder. Primes, gcds, congruences and modular inverses build up to RSA — which is generated, used and then broken here on primes small enough to check by hand.
Overview
By the end you can compute in modular arithmetic confidently, judge the parameters of the everyday systems built on it, and explain exactly what RSA's security rests on.
Division, Euclid, extended Euclid, fast exponentiation. Each with its trace, so the method transfers to paper.
Decide solvability, count the solutions, and find them — including simultaneous systems by the Chinese remainder theorem.
Reduce enormous exponents to small ones, and know exactly which hypotheses each theorem needs.
Generate a key, encrypt and decrypt, and then recover the private key by factoring — which is what shows what the security actually depends on.
Choose a hash modulus and say why a power of two fails, check the three conditions that give a generator full period, and validate an affine key — then break one from two letter frequencies.
Lessons
Divisibility and gcd come first, then modular arithmetic, and last the applications that use all of it.
Proof technique and induction.
Use the workbench lab in every lesson. Each mode prints the algorithm's trace rather than only its answer, and the point is to be able to reproduce the trace on paper afterwards. Every lab opens on its own lesson's example, so the first figure on the screen is one the text above it already states; change one input and watch which lines move.
Do the RSA lesson with the primes it starts with, then change them. Watching the key change and the ciphertext change with it is what makes the mechanism concrete.
Take the factoring demonstration in “RSA Encryption” seriously. The lab breaks the key it just generated, and understanding why that is easy here and hard in practice is the whole security argument.
Analytic number theory: the prime number theorem is quoted in “The Sieve of Eratosthenes” and not proved, and the Riemann hypothesis is mentioned only as context.
Elliptic curves, discrete logarithms and Diffie–Hellman. RSA is the one public-key system developed here.
Cryptographic engineering: padding schemes, key management, side channels and protocol design. “RSA Encryption” is the mathematics of RSA, and textbook RSA is not a system anyone should deploy.