Gotcha!, I believe that I can explain why Exerelin compatibility is broken for v1.1.0; for that matter, it applies to the Bushi v1.1.0 update as well.
In Exerelin v0.6's 'ExerelinData.java', there are the following lines:
// Test for Bushi
if(isFactionInstalled("bushi", "data.scripts.world.BushiGen"))
possibleFactionList.add("bushi");
// Test for Hiigaran Descendents
if(isFactionInstalled("hiigaran_descendants", "data.scripts.world.HiigaraGen"))
possibleFactionList.add("hiigaran_descendants");
When you updated both of these mods, Exerelin's built-in check for other mod(s) installation no longer detected those files, as you renamed them ('HiigaraGen.java' became 'HiiPolarisGen.java', and 'BushiGen.java' became 'BushiSeiikiGen.java'), thus the factions are no longer selectable.
A simple pair of text edit(s) to 'ExerelinData.java' took care of that, but sadly more than a few end-users are just a tad clueless on how to do just that, or so it seems.
Addendum: I'd recommend re-naming the Hiigaran Descendants' versions of the Pulsar Beam and Flak Cannon; the former name is taken up in FlashFrozen's Neutrino Corp. mod as well, and the latter is part of vanilla StarSector.
I just added a (Hiigaaran) suffix onto each entry in the 'Name' field of this mod's 'weapon_data.csv', but hey, that's just me.
Since you updated Hiigaran, did you Comment out the mod_Json again?
If you did not it will not work.
Plasmatic, that particular step is no longer necessary, as Vayra was the first to demonstrate an alternate edit to <ModName>ModPlugin.java that bypasses that issue (followed shortly after by MShadowy, and now Gotcha!)