stevec: Well, i was in you position a few months ago, and i faced this same dilemma, as i had obtained my carts from a recycling bin, and they were dried out. You should flush all of your carts, especially your pigment blacks, as these can clog severely.
When i was flushing the carts, the dye colours flushed out quite easily, but the pigment black took a few repeated washings. I just drilled a small hole in the ink tank, connected a home-made device to the ink outlet port and flushed it with my hose outside. I flushed in both directions ( ie water in through ink port, out through drill hole, and water in through drill hole and out through ink port). There is a video of someone flushing a dye cart somewhere on the forums, but i cant remember where. You need to flush throughly, but dont use too high pressure, else the sponge may come dislodged.
I then filled a few syringes with distilled water, and flushed out the cart, pushing water throug the drill hole and out through the ink port. This was to ensure that no disoolved minerals remained in the cart, even though my water is pretty soft. After that, i filled the syringe with air, blocked off the air vent at the top of the sponge compartment, and pushed air through the cartridge, to push out the excess water. After that, i left it to dry for a few days untill it was bone dry (i didnt use the method of using a humectant / sponge conditioner).
To refill, i sealed off the ink exit port with the orange clip, and filled the ink tank. I then sealed it with hot glue. On hindsight, i would have been easier for me to seal the empty tank and then fill it via the durchstich / german method, and this is what i shall do for any more carts that i obtain.
As the carts were dry, i let the ink soak in and diffuse for a few days before i used them.
I have been using them in my IP3500 for a few months now, and i am very happy with the results.
I dont believe the durchstich method damages the sponge (or it damages it only an infinitismally small amount) as i have had no problems with ink leakage or print errors (but then again, i have only refilled it via the durchstich method 2 times). It is also so much easier when compared to the traditional method. If you want more advice, i believe there are a lot of threads on the forum concerning the effect of the needle on the sponge.
Good luck!