I just went through the same thing with a pair of Simms Gore-Tex waders that had gone nearly ten years without leaking. In better economic days I was almost wishing they would die so I could get some with built-in gravel guards and other conveniences, but in today's climate, I'd rather see if I can repair them and defer the purchase.

The link that Stage1 posted is basically the process I followed and would recommend. There's also an excellent video on the Simms site (http://www.simmsfishing.com/site/repairs_main_new.html) that shows the process even better. I'd long heard about rubbing alcohol to expose the pinhole leaks but had never heard about the idea of using a spray bottle until I saw the video. Man, did it make all the difference in the world. I turned mine inside out, hung them from a hanger in a doorway and sprayed them thoroughly with the alcohol. Within a few seconds, every small hole showed up as a gray dot. Rather than try to treat them all real quick while the waders were still wet, I took a pencil and traced a light circle around each. In my case, I went ahead and let the waders dry and then came back at my leisure and rubbed a small amount of AquaSeal into each spot. Works like a champ.

Simms suggests in the video, and I would have to agree with the thinking, that you NOT fill your waders with water more than a modest amount to test for bootfoot leaks. Otherwise you're risking putting too much pressure on the seams from the weight of all that water and creating a bigger problem than you'll ever be able to fix. Try the method above. I'd be willing to bet you've got more holes than you realized!