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Hey, unless I've got things really wrong, those four bolts with the white threadlock are for mounting the two disc caliper adapters to the frame. And then the four bolts with red threadlock are for mounting the caliper to the adapter.
No Di2 blanking things for me either. I also think only getting the one little clip on hose clamp is a bit weird, as there are (as far as I can tell) two places for them to clip onto, one on the fork and one on the chainstay. Those are as well as the little bolt on hose clamp.
How's your build coming along, anyway?
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unless I've got things really wrong
I think you probably have. The M6 screws with the red compound are for mounting the adapters, the caliper mounting screws should be in the caliper box. The M5 screws with the white compound are the bottle cage screws, short ones for just the cage and long ones for the cage + Di2 battery holder thingy.
Mine came with them, you can see the 4 of them top left of this inner-parts-box picture:
Did you got some Di2 blanking grommets/plugs? I didn't get them, and emailed bruce@upgradebikes.co.uk about still waiting for a response.. Try your luck asking him about those screws.