I'm convinced on the making them shorter vs. bone toughening question. Changing my vote to Make Shorter. I'm not 100% sure on respiratory efficiency vs. pressurized lungs. Do we have gene samples available for more efficient lungs? Something to look into. As for ectothermy, normally I would be all for it if we were designing a creature from the ground up, but in this case it seems really impractical. Consider:
1. We'd need to redo the hypothalamus to not change body temperature while still producing the required hormones that the body needs. Which means complicated and potentially dangerous brain DNA alterations.
2. We'd need to rework a bunch of proteins to accept a wider tolerance for core body temperature than is normal in humans. Again, that is a lot of work.
3. We'd have to rework the histamine response to neither cause fevers (which are not available for ectotherms) nor to rely on them in the immune system. And we can't change the histamine molecule itself, since it's also used as a neurotransmitter and for other immune system responses.
4. Beacause of 2 and 3, that means we have to basically redo the entire immune system to use different proteins, not need fever to drive out bacteria, to be more pro-active about killing bacteria to compensate for higher infection rates, but not kill of vital gut bacteria, etc.
5. Basically, what RAM said. Making them cold-blooded would mean periods of lethargy in cold, periodic sunning requirements, a change in sexual response not to get squicked out by feeling up cold flesh, and a host of other psychological changes to make the colonists feel OK about being lizard people and not become super depressed.