Yeah you were underleveled almost for sure.
Honestly my only complaint about the YHVH fight was it dragged on far longer than it needed to. Didn't help that the fight technically began with reaching the Holy Grail, losing to that, unmasking Igor, saving your friends, then the Miniboss Rush before fighting the Holy Grail again (with a stupid long "cut the veins" sequence at the start) and only THEN did you get to YHVH.