Question: Still, his report raises potent questions about the Torah codes methodology, questions even Rips acknowledges to be serious.
Nobody can question the Torah codes methodology, it is perfect.

Answer: no

Question: Who's the other cup for? inquired Julius.
There were two of them there, but three cups set out.

Answer: it is not possible to tell

Question: On Sundays it switches to small pets, especially caged birds.
Caged birds are mostly used on Sundays, because they change to small pets.

Answer:
yes