Joining a game with friends is much easier than finding a compatible pub, but it is not as simple as with vanilla Torchlight 2. Finding games with the right combination of mods can be difficult, to say the least. Finding public games with mods you're interested in playing with requires choosing mod collections at the top of the internet lobby and seeing what is available. Joining your friends' games and joining pub games are entirely different ballparks due to the mod list and order system. Sometimes these recommendations will be found in the comments section, and sometimes they are found in the mod loader. Be sure to read the mod's page on the Steam Workshop to see if the author recommends a particular placement.
Some mods do not require that they be in any particular position, but some do. Make sure that everyone launches the game with mods and not the vanilla client.Make a list of mods to give anyone joining your game and give the priority order to avoid compatibility issues.Everyone will have to sync to the host when they try to join a game, but you can iron out several connectivity kinks by having everyone download each mod before they launch the game.This is basically to save myself some time, and hopefully save a few of you some headaches as well. I can only assume other people are having issues with mods and multiplayer considering how many times I've had to explain this process over the past week.