I've done my fair share of JK spamming for CR, but since the missions update I've been wondering what the most profitable portions of the clockworks is. I've noticed that as far as missions go, the biggest money maker (excluding mats or tokens) is mission 7-2-3, the T3 wolver/jelly arena. Which can earn me 3300 average at the cost of 30 energy, a 1.2k CR profit per run assuming 7k CR CE price. Unless clockwork runs have had a profit increase, spamming mission 7-2-3 seems to be the best option.
However my method is open (and hoping for) scrutiny, if there's a better CR making pattern out there, please post.
Also, just to clarify:
"total delve CR income" - "number of elevators taken" x "current CE price" / 10 = "CR income"