I am in accounting and I love playing with numbers so here is what I came up with for you to compare.
3 day ph from way.com: Adult $240. Child $230
3 day 1 park per day from way.com: Adult $206. Child $195
Sea World weekend 1 day visit: Adult $64. Child $64
Sea World weekday 1 day visit: Adult $50. Child $50
San Diego Zoo (promo code 14043) 1 day visit: Adult $40. Child $30
Now to compare:
City Pass with Zoo add on: Adult $367. Child $315
SW weekend/Zoo/3 day ph: Adult $344. Child $324
SW weekday/Zoo/3 day ph: Adult $330. Child $310
SW weekend/Zoo/3 day 1 park per day: Adult $310. Child $289
SW weekday/Zoo/3 day 1 park per day: Adult $296. Child $275
Universal Studios are priced at Adult $87. Child $79. So if you are planning to go here too then the City Pass is a good deal. But if you are not planning on going to Universal then I would purchase your tickets separately for adults, however the child City Pass is cheaper if you are doing the 3 day ph and Sea World on a weekend.
I have never purchased a 3 day one park per day and then tried to upgrade it to a park hopper on the last day so I can't help you with that question, sorry. You can however call
Disneyland and ask them how much they would charge.
One more thing, I have used Way.com a few times and they are great. Never had a problem with them, just don't wait until the last minute to order the tickets. Once I had them emailed within a few hours and another time it took two days.