The issue of getting good quality rims would appear to be less moot these days with 29-er wheels.

However, in my experience, Mavic 719A rims are excellent -- they're used in 32H spec on our tandem, and we have them on each of our touring bikes.

If you think you are capable of relacing the new rims on to the old hubs, give it a go. All you have to do is tape the new rim to the old, undo the spokes, transfer them across to the corresponding new holes, true the wheel, and you are good to go. No worries about which holes in the hub. You do, however, have to make sure you have the correct number of holes in the new rim. Even transferring over the rim tape shouldn't be a major issue, whether it is adhesive or not.