You have three points, AP1/2/3/ Which one, or are all of them, an MSR4k? You're right, the planner error dialog box isn't doing a good job of telling you which radio to adjust the antenna for. it was a consequence of shoehorning in the 4-radio AP into the first revision of the outdoor planner.
So a few things,
* Even with a 1dB design margin, the outdoor planner won't build a mesh link using the D607 at or near 1km. For 1km or more, you need to either use the ANT-2x2-5010 (not ideal) or the ANT-2x2-5614. See attachment 'ap175-700m-ptp-test-fail.png' for a screenshot of my attempt of a 700m PtP shot with the D607 with AP-175s. In short, the D607s just don't have enough oomph to get you there. You need higher gain antennas. See below for more.
* When you let the planner automagically select the mesh links for you, it assumes that any link (portal+point+point(s)) all need to be able to see each other in some way. If it can't then it throws out all those wacky alignment errors trying to get an adjustment to come close. Remember, the tool is not only looking for SNR, but useable SNR above the noise floor. If there's not enough separation there, based on the link distance, antenna gain, design margin, and noise floor, the link won't be stable.
* The best way to control what the planner does in a multi-hop plan, is to control the channels of the links. In your case, you have three 4-radio APs, RADIO0 for client access, and then each AP can build two other links to its neighbors (Radio 1 and Radio 2).
I built it like this:
AP1
Radio 1 Portal @ 141deg --> AP2 Radio 1 Point
Radio 2 Portal @ 96deg --> AP3 Radio 1 Point
AP2
Radio 1 Point @ 327deg --> AP1 Radio 1 Portal
Radio 2 Point @ 48deg --> AP3 Radio 2 Portal
AP3
Radio 1 Point @ 275deg --> AP1 Radio 2 Portal
Radio 2 Portal @ 227deg --> AP2 Radio 2 Point
So with this, you have up to three mesh link. I took your layout, and built a different channel per link on the map and assigned accordingly. That way the planner is forced to build it the way I want it to, instead of it trying to think FOR me. See attachment '1-config.png' for the examples.
Attached is a zip file with two KMZ, one using ANT-2x2-5010 which gives you anywhere from 47Mbps to 64Mbps (using a 3dB margin, I am assuming this is all clear line of sight); and then the ANT-2x2-5614 which gives you 77Mbps to 127Mbps (again, with a 3dB margin). Hope this helps, but I wouldn't plan on getting the D607s to work at that distance.
And yes, while I have a feature request in to change the erroneous error you are seeing (or if the link is REALLY bad it just never comes up at all) and replacing it with a clear warning that 'the link is too far to build a stable connection' kind of message. We are working on later version that will correct a lot of this behavior. Thank you for your patience.
TL;DR - You need higher gain antennas. :)