1. The phone call is obviously from Randal. He's telling you that his old personality was emerging, the one that was weak and abused. That's the person calling. That Randall is "prefectly fine" after the call just means he "got back" to the newer Randal.
2. Like many others said: certainly Golgotha. The way he sees things and draws those figures. He also understands and likes Markus. The way he describes his siring also hints that he went off the rails pretty much immediately, there's really no reason for that to happen if he was Iscari.
3. I was defnitely thinking about stigmata. The vampires heal constantly, so there's most likely no reason to actually have them bandaged, even if there were spontaneous wounds or Randal did them himself again and again. It's probably a mental thing for Randal, maybe he feels the wounds.
2&3 Golgotha is the place were Jesus was crucified. These allegories aren't exactly subtle ;) The special ending is pretty much "suffering Jesus becoming the Antichrist".
The ending is chilling. It's well done. Argent Games has done some other VNs that remind me of Nitro+Chiral games and they are also very disturbing. These are not happy dating sims. I wouldn't mind a couple of variants of this special ending, but I think it's the most effective in this way. If, for example, the MC was on his side willingly, as a couple even, it wouldn't be as devastating as seeing Randal become everything he hates and even completely loathing the person he fell in love with.