I find it a bit odd that you're so worried about the $12/day parking but are/were contemplating spending a significantly more amount of money on the 3rd day park hopper.
But aside from that, if you follow what both Bruce and Mousechild said - you'll be fine. Echoing Mousechild's thoughts, Disneyland - especially if you're going for 2 or more days - isn't about an obsessive-compulsive game plan: it's about atmosphere and enjoying what you can. Also, if you have 2 or 3 days, Magic Morning or not, you won't be wearing you or your wife out - even if you spend all day everyday at the parks. With the time allotment you have you can easily spend time in the shows and even taking coffee/soda breaks throughout the day; you won't need to be running and game-planning every second.
On my last visit - which I spent a large amount of money on, too - I only had one day at the park. Thankfully it was a cold and rainy Friday so the crowds were non-existent. I did walk a ton, go to every major attraction and several smaller ones in both parks, and I was worn out the next day. If I would have had 2 or 3 days I would have spent them all at the parks, but would have taken my pace much easier.
If you stay somewhere near the parks on the transit line, or close enough that you can walk across the street to DL, then you can also go every morning and evening/night and return to the hotel for a mid-day nap and swim. You'll be surprised at how relaxing and revitalzing that really is.
But going to the parks in four-hour increments, and using the free 3 hr DD parking, really isn't worth it, period. By doing this you'll be doing just as much running around and game-planning during each brief increment as you would have doing just one day, kind of defeating your purpose. The end result is that you'll have spent hundreds of dollars for $94 worth of time in the park, and in the end still feel cheated that even though you seemingly spent 3 days in Anaheim you didn't really get to see/do much of anything.