Current setup:
53 X 39 chain rings
12 X 27 cassette

Will occasionally switch to a 11 X 23 cassette.

I've been told that the rear jockey wheels should be perpendicular to the floor when in the big/small combo. However, as can be seen in the pics below it's not. So, when I install my new chain do I make it the same length as the old chain that's on there or do I make it so the jockey wheels line up perpendicular?

1st pic shows how the jockey wheels line up with a plumb-bob currently. 2nd pic shows how the current chain looks when the jockey wheels line up perendicular. Not sure how many links that would translate to but it looks like a big sag.