Welp, I kind of lost interest in maintaining this too. I never got any feedback, and didn't have the opportunity to test it in multiplayer, so it's quite possible that my Oculus fixes introduced the issues that you've observed.
Rook's code was untouched in 1.03, and that chain link bug you saw is related to Demigod's many inherent beam / chain issues (some of which I fixed in Oculus' Chain Lightning ability, though those fixes would relate in no way to Rook's towers).
Took a quick look at Oculus' code, and Brain Storm is hardly touched at all? I recall testing it and having no problems / log errors. The only way it could have zero cooldown from the changes I made is if it's somehow now throwing an error, which will prevent the rest of the ability cleanup code from running.
Incidentally, I just noticed that Brain Storm clears debuffs on the Oculus who is casting it, rather than on the target. Is that intended? Isn't it supposed to clear the target's debuffs?
The only other Oculus functions that are modified in 1.03 are Chain Lightning (effects/sticky lightning fix), Lightning Blast (friendly fire disabled), and Ball Lightning summoning (attack move fix). None of these could result in Oculus being made invisible; how often did this happen, and was it reliably linked to a particular ability use?
Edit: Oh, well, I never did test the change I made to his character (model/animation) blueprint. All I did was translate Ptarth's changes into non-destructive form, and I confirmed that the correct variables were being changed, but I never tested the result. If I messed this up somehow, it could mean that his invulnerability mesh is broken, and his model might be disappearing when he's made invulnerable by Shield / Orb of Defiance.
Of course, if there's no interest in using 1.03 version in the tournament or if the tournament is already over, then I don't really care to fix it at this point, since the community is pretty much dead otherwise.