Barney uses a small white machine that extrudes a very long pipe. This is not a special effect. The "pipe" is a flat strip of spring steel which has been preformed into a tube. The strip is flattened and wound around a reel inside the machine. As it is unwound it forms itself into a tube. When retracted it is again flattened and wound on the reel.
When the prop man was unable to provide mosquitoes for the scene in which the impostor Cardinal is bit, one of the nuns at the Mount St. Mary's College filming location mentioned that the biology department had an ample supply of mosquitoes, as it was conducting experiments. She gave them a jarful. But just prior to filming the scene, the prop man received a frantic call from the college informing him not to use them, as the batch he received was malarial mosquitoes.
The monastery's exteriors were filmed at Mount St. Mary's College in Los Angeles which had been used previously for the hotel's exterior in the pilot (S1E1) and again in "Operation Heart" (S2E7) for the hospital's exteriors.
After Rollin enters the impostor's room posing as a Cardinal, he glares at Major Felder when she fails to genuflect and kiss his ring. The camera focuses on Phelps who smirks slightly at her "dereliction of duty".