Say I have 5 CPs on my target and 3 Anticipation stacks. I decide to use 1 more SS to get me to the next BG level. RS effect procs and I get 2 more stacks of Anticipation. I use a finisher and I get the 5 stacks of Anticipation as active CPs on my target. Thing is I loose the extra CP from Ruthlessness. Correct?
If that is the case, then do I never go above 3 stacks of Anticipation or the lost CP worths the 1 - boosted from higher level of BG- finisher?
Correct, but for your second question, 4 should be fine. 1 proc + 4 will just put you back at 5 CP, only 5 AP should actually clip the effect (unless I've missed a broken mechanic), meaning you could still use an ability at 2 even though you might hit 4, without worrying about lost CP.
(edit: excepting under Shadow Blades, as mentioned below)