Just an update. Contacted Merlin and they are going to send me a set of the missing pads. But they are waiting for Hope to ship to them, and then to me. Since it will be a while to get them I went ahead and ordered a set of the Hope E4 brake pads. Turns out they won't fit, too big.
I started poking around the internet and found out the Shimano version of the flat mount RX4 calipers are bigger than the Sram flat mount RX4 calipers. This explains why I got the wrong size bore caps. The Sram calipers use brake pad HBSP359 which, as mentioned, is smaller than the E4. Somehow I downloaded the wrong pdf file and ordered parts for the Shimano calipers. My fault.
So, I now have a set of purple bore caps, installation tools, and organic brake pads for calipers that I don't own. The pads I can return to Jensen. Will need to talk to the shop about exchanging the bore caps for the correct size.
I guess for now I'll just have to deal with the noisy rear brakes. I ordered another set of pads from a different source, they should be here next week.