I'm still working on this, and will post more details when I've made more progress. It's definitely turning into a bigger project, but I think it will be worth it.

I've also made a slight adjustment to hit locations, modeling them after the rules from The Riddle of Steel. We're keeping the same zones (Arm, Body, Head, Legs), but rather than randomly determining where you hit, you decide which zone you're going for, and how you're attacking. For instance, if you want to attack the Body with a power sword, there are multiple ways to do it — an overhand swing, a horizontal swing, or maybe an upward swing. Each of those locations will most likely hit the chest, but could the defender can cause the attack to "wander" into a different, less fatal zone.

I'm also making some major changes to Wounds/Critical Damage, and Psychic Powers.

Here's my plan on how to handle the Colony Characteristics:
 
Complacency
While Complacency is greater than Size, the crew benefits from +10 Morale. When Complacency is reduced to 0, Order and Productivity decrease by 1d5.  
Order:
While Order is greater than size, all Command Tests to the crew benefit from a +10 Bonus. Also, its Productivity increases by 1. When Order is reduced to 0, the crew suffers -30 to Morale.  
Productivity:
While Productivity is greater than size, all Ship Actions benefit from a +10 Bonus. When Productivity is reduced to 0, the Ship counts as being Crippled.  
Piety:
While Piety is greater than Size, Order and Complacency are increased by 1. When Piety is reduced to 0, Order and Complacency are reduced by 1d5. Until the problem is fixed, rolls on the Warp Travel Encounters happen once for every 3 days of warp travel, rather than 5 (due to less protection from the God-Emperor . . . sinners.) Note that none of these affect Profit Factor. I've decided not to have the ship affect profit factor at all. I'll leave that to regular Colonies, and all of the cool stuff the players do.
 
Anyhow, feel free to offer suggestions or other ideas on how to work things.

Although, when I started reading this thread, I had no doubts about the purpose of RT games and how awesome the game is, at the end of it now I feel like I've gained some real insights as to how the game is to function.
I once heard author Tracy Hickman say, in reference to rpgs, that they are not about getting old and getting lots of stuff. That's what life is about.
Even thought I though I had a clue as to what RT was about, I think, until I read this thread, that I had the wrong idea. I was still wondering exactly what to do, seeing as we already had all of the stuff we needed. I had forgotten that acquisition of such goods is not the point of the game. It's having fun. And, when you're a mighty Rogue Trader, having fun means a lot more than it does for a level 3 Warrior with a +2 Broadsword.
In my groups sessions, we've found the most fun when characters are working after their own agenda's. Our first two sessions were completely devoid of this. The characters did what they were supposed to, went to the right locations, found the right information, and generally followed the path of least resistance. In our third session, however, one character finally did something outrageous that set the ball in motion. When faced with a problem, he went with the absurd solution that everyone had joked about, but had quickly set aside as 'too far'. At that moment, the game left linear play and entered sandbox mode.
They stopped worrying about 'getting old' (following a linear story line) and 'getting lots of stuff' (not taking risks), and went after what they wanted to do, and what would provide the most fun for them.
Rogue Trader, in my opinion, is about having fun. When you're already at the power of a Rogue Trader, 'fun' has a lot more options.