I've found the spawning grounds and have piranha attacking me but shooting, right clicking, left clicking nothing seems to collect/kill so I can collect the roe to get started...

Kill spawning grounds and collect the roe as loot. You probably just didn't notice roe against the backdrop of the corpse.

I did find the spawner itself, even had a big green retical over it but shooting (even shift+shoot) didn't destroy it. Not sure if it matters but I was using the shotgun. Will have to try again with the rifle perhaps?

Okay, so rifle still didn't hit the spawner. I was able to unequip all weapons and melee the spawner down to get roe. This could be a compatibility issue with KS_Combat_Updated 1.2.8 since it changes the way bullets shoot I believe.

It's probably related to your mods, yes. I shot at the spawner with a pistol, a machine gun, and a nuclear warhead xd, and it died