Sorry if this is a dumb question, but I'm not quite sure about the Program prices listed on pg 228.

Would a Common Use Program be:

Rating1: 50¥; R2: 100¥; R3: 150¥; R4: 400¥; R5: 500¥; R6: 600¥

or

Rating1: 50¥; R2: 100¥; R3: 150¥; R4: 250¥; R5: 350¥; R6: 450¥

First one. It's a simple stepped multiplacation problem; don't make it more complicated than it has to be. The rules complicate themselves enough already (take a look at the skill cap rules for details on this )