Congratulations on almost finishing your residency!!!
It seems like just a little while ago that you were taking your toddler boys to WDW when you started your residency.
We just got back on March 31 and I meant to take pictures (did on a few rides). It's hard to do though while you are getting on. I should look look at which things I have pictures of and get some posted.
You probably don't need a GAC; having wheelchairs will allow you to use the wheelchair accessible entrances, no matter where they are. If you find you have problems, you can always got to Guest Services in any of the parks and explain your difficulties.
Disneyland is a lot different than WDW, in that most of the lines at DL are not accessible, so the wheelchair entrance for most rides is at the exit. For a while they were requiring wheelchair users at DL to get a card to use the wheelchair entrances. Now they are in the midst of changing from a Special Assistance Card (where everyone got the same treatment and used the wheelchair entrances, regardless of need) to a needs-based GAC similar to what WDW has.
If you bring the wheelchairs in line with you, they will generally be waiting close to the exit. Many of the rides with moving walkways have wheelchair users board at the exit. Except for Peter Pan, they can slow or stop the moving walkway. You can also bring the wheelchair as close as you want to the ride car. For example, on HM and Spaceship Earth, we used to leave DD's wheelchair outside (about 20-30 feet from the boarding area). As she's gotten bigger and heavier (and we worried more about falling with her), we've brought the wheelchair closer in, so that it's only a few feet from the ride car, with the wheelchair actually on the moving walkway. The CMs will move the wheelchair out of the way after you are in.
Here's a link to a past thread about boarding.
Sometimes, you get on the ride in one place and get off in another (or on the other side of the track), In those cases, the CM will move the wheelchair so that it's where you get off.
Since you have 2 with wheelchairs and they can transfer, I think you are wise to avoid the wheelchair cars (although it's still an option if one of your boys gets to tired to transfer). You generally have to wait longer for the wheelchair car and for lots of things (like Pooh and Buzz) there is only one wheelchair car.
For Pirates, the entrance is upstairs in one area and the exit is down one floor and a long ways away. like Bill mentiones, you can bring a folding wheelchair right into the boat. They just put it behind you. We have even put DD's non-folding (well, it folds with a lot of trouble and dis-assembly) onto the boat. They can do that if the wheelchair is not too havey or bulky. They also have folding manual wheelchairs at the entrance that you can trade your wheelchairs for. Two of your boys could probably ride in one together if they had to. They fold that up, schlep it into the boat with you and then at then end you can use that to get to your own wheelchair.
For Goofy's Barnstormer, you can bring the wheelchairs into the regular line with you (it doesn't look like it, but you can). You board on one side of the track and after you are on, the CM lifts the wheelchair to the other side of the track so it's waiting when you get out on that side.
If they want to ride Test Track, you can use the regular boarding area (where you step down to board) or there is a level transfer point that 's more like getting into a bathtub. I highly recommend that since you have as much time as needed to baord without lots of people observing the process (plus, it's easier than stepping down).
Up until about 3 years ago, we did take DD on Peter Pan. It was not easy though since she can only walk when fully supported and DH was carrying her on. Once she hit 80 pounds (and DH almost hit the wall getting off with her), we decided no more Peter Pan. The wheelchair can wait in the exit area where you get on. But without being able to stop the moving walkway, it's still tough.
One ride that I would recommend against (or at least you ride it first) is the Primeval Whirl at AK. It's kind of a combination of teacups and roller coaster. My DD alsmost spun out of that one. My older DD (who does not have any disabilities) found she needed her feet and arms to brace herself and keep in place. My younger DD has pretty good trunk control, but goes into extension when excited, unless her feet are strapped down. By the end of the ride, her butt was barely on the seat.