I have no actual answer for you to get to precise landing calculations. But we may be able to nail it down closer then Cuba.
First of all, can you use the trajectories mod in RSS still for calculatinr orbital Trajectories?
The reason you land short is because of Earths rotational speed while being on a inclined trajectory. So even although you may be able to land near or exact to the location based on a orbital trajectory calculation the rotation of earth shifts your surface landing area when your orbit is inclined against the landing target.
You know this ofcourse, the reason I'm telling is because I want to ask if this is the only parameter that causes you to land off target.
Can you confirm this, can others confirm this?
You could try the following.
If it is the only reason for missing your target then what you may do is use a maneouvre node where you'll retro burn to calculate the amount of time from a set maneouvre node to the KSC (let's say it's 50 minutes).
First do a hyperedit test and see how much time is added to that maneouvre node calculation in actual flight time. Because the actual flight time will take longer because of aerobraking.
If you do that you'll only know the added time for aerobraking under the same descend profile and it will never be the same exactly depending on your maneouvring through the atmosphere but you may be able to nail it down within 10-20 seconds difference. Let's say the maneouvre node said 50 minutes, and a static descend profile test get's it to 52minutes and 30 seconds.
Now calculate how much the earth surface would have rotated in 52 minutes and 30 seconds. Thats 3150seconds!
3150 x 465.1 = 1451112 meters. Which is 1451.1112 kilometres. Your landing in Cuba seems plausible depending on your time through the atmosphere from your maneouvre and to land.
This method does assume there still is a Trajectories mod function for orbital calculations for RSS or any similar mod, and I don't think it covers everything to make your precise landing. But it will probably get you closer to KSC then Cuba.
You may also want to calculate the surface distance change in case you land at a target on a higher or lower latitude as they will have a slower surface speed. I'm not sure how exactly the KSC is located on the equator, meaning whether it is exact. But land anywhere else and you have to deduct earths rotational surface speed since the constant of it is based on that of the equator.
As for knowing how to calculate the distance needed for aerobraking to know whether you land long or short, I don't know. In any case it seems a very hard thing to do in RSS. I wouldn't even try it. If your shuttle is capable of steeper descends, coming in from a higher alttitude on a steep aerobrake descend can make for a more precision landing. The question is, how steep of a descrend profile and your shuttle take without exploding into pieces.
