I'm very sorry to hear about your keycaps not fitting. The stem holes on all my keys are actually quite a bit larger than a Cherry MX switch by design, because of course it's much easier to make a loose keycap fit properly than it is to loosen a keycap that's too tight. When printed in plastic, all of my keys either fit properly or can be made to fit properly with a simple solution (a small piece of scotch tape: https://i.imgur.com/poLbH.jpg). However, as you have noted here, in this case for metal it seems there is still residue in the stem hole and the hole itself may even be too small (although I can't tell from the picture).
Unfortunately, my best advice to you is to take the most obvious next step--continue trying to scrape out the plastic residue with a sharp pick and, if necessary, try to file down the + hole until the keys fit properly. An X-ACTO knife, pick tool, or perhaps a very small drill bit may be good for removing the residue and opening up the stem hole. Be careful about trying to install the key if it is too tight, because there is a chance the switch will be pulled from its housing if you try to remove the keycap.
I'm afraid there's not much I can do for you myself, as I am simply the designer, not the manufacturer. I do not handle payment, shipping, warranty, etc. You can certainly contact Shapeways' customer service and claim you received a defective product since these keycaps are known to work when printed in other materials. In fact, I've even had some customers who ordered more than one of the same keycap in metal claim that some fit and others didn't, which is a clear indication that Shapeways has some inconsistency in their products. But they will probably try to play the caveat emptor card, since 3D printing is not an exact science.
I hope my response has been at least somewhat informative/helpful and sufficiently prompt. Please let me know if you still have questions or concerns, and I wish you the best of luck in sorting out this issue.