Honestly, I would not try to clean the blocks before putting them together into a quilt. You have no idea how the different fabrics might shrink, and just soaking them in water could be enough to introduce tons of distortion into the blocks. I would make the quilt first. Quilting stabilizes fabrics so that they cannot shrink wildly the way they can when washed on their own. The quilting stitches bind the fabric to the batting, transferring control of shrinkage to the batting. In other words, the batting in a quilt will not let an 18" block distort. Soaking an 18" block of old fabric in water, on the other hand, could result in shrinkage of an inch or more in one direction and none in the other, or turn the entire block into a "wonky" block -- especially with applique, which can bubble and distort differently than the underlying background fabric.
If the blocks smell so bad you cannot work with them, I would encase them in a plastic bag with Odoreaters shoe insoles with charcoal (or some other odor absorbing type material) for a couple of weeks.
Once the quilt is actually quilted and bound, I would just try washing normally in a manner suitable for quilts -- meaning in a washing machine that uses a ***lot*** of water so any dye bleeds are quickly diluted, and not allowing the machine to agitate. Turn off machine, hand agitate, then spin. There are good threads on the QB about how to safely wash a quilt for the first time in case there is dye bleeding. If you do this and the dyes don't bleed but you still have oldish stains, then I would use Retro Clean (
http://www.retroclean.com ). Retro Clean requires soaking, and you really do not want to soak a quilt unless you are pretty sure nothing is going to bleed.