Wow, does it really increase it that much? I didn't know that. Does it balance out that we've got max HP as well? Yeah, those bite and claw attacks really cut us down, not including the Powerful Charge it had on it. I think in one round, by one of them, I was taken down by a good 45 points of damage, and he rolled low on the dice. I think they had something like +24 to hit. Not hard considering they're colossal.
I was ECL 13 (with 11 lvls), which is actually higher than what others had (the Favored Soul only had 10).
No, it doesn't. The reason is that every encounter he throws at you will be at max HP with no resource expenditure, whereas you almost always have to heal up after every encounter. You're fighting 4 encounters/day, and each of the enemies in those encounters will be fresh and ready to fight, whereas you won't be after the first.
From the sounds of it, if they did have 40HD, they only have a 14 Str or so. Size category decreases attack bonus, and Aberrations have Cleric BAB. So +22 BAB, with a 14 Str. That honestly doesn't sound right, so their stats are fairly high, and their HD are around 30 or so. Even still, this is well above a CR 15 for an Aberration.
Edit: You need to get him to these boards so we can educate him. If he even had a slight grasp of optimization, both tactically and stat-wise, he wouldn't suck nearly as bad as he is and wouldn't have to house rule everything so much.