It sounds like you have this system programmed as convential and not MotoTrbo. As far as the LCN's go, just put in the known frequencies lowest to highest, label each LCN 1,2,3 and start there. If you get this programmed correctly, and you're missing conversations, switch around the LCN's. With only 3, it should be easy to figure out.
With the DMR flashing, you might have to program it as a one channel DMR if this doesn't work. ID Search must be on in both programming options, the system must be set to on and I think that's all you need, the System Quick key must be on to scan in ID search.
Might also want to download Firmware 1.11.18 that's available if you know how to upload via a BIN file. If not, just wait...there's a difference with CAP+ receiving between versions I noticed.