for (int i = 0, j = i % strlen(user_input); i < strlen(plaintext); i++)

for (int i = 0, j = i % strlen(user_input); i < strlen(plaintext); i++) {
  ..
  j++; // or any change that you want to have in j like j =i+2
       // j = i%2
}

size_t len1 = strlen(user_input);
   size_t len2 = strlen(plaintext);
   for (size_t i = 0, j = i % len1; i < len2; i++) {
      ..
      j++; // or any change that you want to have in j like j =i+2
           // j = i%2
    }