Technically, you are already getting more hit points since the Template and Prestige Classes that everybody has grants stat bonuses which include CON increases, which equals an extra +1 hp / die for every even multiple of CON above 10. Your +3 ECL-ness comes from all of the other bennies (Stat Increases, Natural Armor, Breath Weapon, immunities, unarmed attacks, etc.). Yew and Kylar, the two fighters, both have 100+ hp.
Y'all already have some fairly impressive ACs and saving throws, which mitigate a lot of damage. The last two times y'all got your collective butts kicked, the enemy knew your group, it's capabilities and tendencies. Y'all wog-stomped the be-jeezus out of the Kenku and Nightmind, the first time around; not to mention the Ten-Eyed God and his minions. There was no Nightmind re-match. "He" had plans, but you didn't seek him out, so nothing came of it.
Really, the only things that really hurt y'all were the Kenku Elite Assassins, the Chronotyryn, and the Spore Bats.
The Sky Pirates ... beaten.
The Spore Bats ... mangled, but victorius.
The Grell ... beaten.
The Ankhegs ... whooped.
The Spider-legged Horror ... beaten.
The Kenku Ninjas ... beaten.
The Temple of the Ten-Eyed God ... beaten.
The Kenku Elite Assassins ... mangled, but victorius.
Nightmind ... beaten.
The Kenku Elite Assassins + Cyrus ... just mangled.
To be fair, the group averages 12th level in all categories except Arcane Magic and Divine Magic (exc. Healing), where you're probably closer to 10th. Your defenses are probably closer to 14th level. Y'all do well against a single opponent, where everybody can concentrate their best on one thing. Y'all absolutely fall apart when you face an organized group. Even one so horribly one dimensional as the Kenku Assassins, whose "divine" magic consisted of a couple of healing potions and "arcane" magic were Elemental Summoning (via Gems) and Javelins of Lightning. Yes, they had very nasty swords, but Dragonbane Unholy Weapons aren't that hard to come by in a world where there is an "evil" dragon theocracy at war with another dragon empire. Breela didn't have much problem avoiding them, she just walked up a tree. Kenku don't fly.
I was amazed that y'all took away one of your biggest assets by choosing to fight in a cave. Y'all could fly. These assassins were only really nasty up close and personal. C'est la vie. I have long since accepted that players will do things that I don't think of. Sometimes they are way cool and I am amazed. Sometime I am amazed in the other direction (in the world of text, my brain goes -- WTF?!).
Regardless, you are correct that there are some imbalances that need to be addressed. I need to figure out which ones are inherent in the v3.5 system and which ones are solely wrought by yours truly. I can fix the latter and only mitigate the former. I do appreciate the input, though.
Anybody else have suggestions?