Ah, alright then. So we're going complex here...
RaptorsVelociraptors should have 6-7 int, as much stealth as you can get (or hide and move silently in 3.5, the camouflage ability/ feat should be helpful here), an extra hit die or two, and +2 dexterity. Maybe throw in 1d6 or 2d6 sneak attack? Not sure what else goes into designing an ambush predator beyond that, but as far as a low-CR critter goes that seems like it might be comprehensive.
IndomidusThe Indomidus Rex, on the other hand, it a different beast entirely. You need to add two claw attacks and a stomp attack (a slam if you can't find a way to scale a stomp) to the T-Rex's multiattack. The indomidus has long arms, uses all of its natural weapons to the greatest effect, and is a mixture between bruiser and ambush predator. It is at least as smart as your average human, and given its ability to formulate tactical takedowns, learn about its imprisonment and the purpose of its tracking chip, and knowing that it could dominate velociraptors, I would give it an int of at least 14, likely closer to 16. Maxed hide and the camouflage trait to demonstrate its ability to literally change its skin color, and then Darkstalker (at least I think that's the name of the feat, it allows you to bypass blindsight, blindsense and pretty much everything but conventional sight) to demonstrate its ability to escape heat sensors.
Hit dice should probably be increased by 6-8 over a T-rex, given how it was able to thrash the big T after a long day of being shot, smacked, ripped into raptors and electrocuted. Natural armor should be 1-2 higher as well, and dexterity should likely be bumped up to 14 (raptor genes and all that).
Its attack plan would probably be to ambush your players, waiting until someone suitably squishy and caster looking passes by it (since it is more than intelligent enough to recognize the threat posed by a magic user)which it multi-attacks and swallows whole. After that, it would tear apart anything stupid enough to engage in melee with it, or go after the next caster character. Just remember, a full attack on anything squishy from this critter will likely lead to "dead on contact" syndrome, so be ready to actually kill player characters when the Indomidus comes around. It would be a disservice to all dinosaurs everywhere if you didn't.
Oh... it probably has a higher CR than the T-Rex, and is most definitely at least Gargantuan, if not Colossal, so be sure to scale its natural weapons appropriately. It definitely has improved crit on that bite attack.