The mod recommendation tool is great for advice just don't let it actually assign mods.
Go to "advanced" and it will recommend which sets to put on each toon (which are normally pretty correct). Click on the little "i" icon in the upper right corner of the "advanced" box and it will show you which secondary stats to look for and which primaries should be on each mod position. It then also gives a 1st 2nd and 3rd best choice for each.
If you don't like what it suggests, feel free to go to Crouching Rancor Mod Advisor. It does pretty much the same but with less detail on secondaries.