We all have had bugs with renegades - i know this.
I guess after the alpha and beta tests,, this is a gamma-test or something.
At the moment i've taken a leave of absense concerning renegades, and i'll pick up the loose ends in a while. i am now working on some other projects. The best advise i can give you now (aside from frequent saving): DIE in mission 3 JUST before you get the victory message, because there's a serious problem from transferring data from mission 3 to mission 4. Normally this data is saved at the end of the mission, but this doesnt happen at the end of mission 3. Somehow, dieing does save the data correctly, so for example, after saving your mission3 near the end, kill off your evac transport (or put it in the garage, since that seems to result in failing as well). BTW: this only works if you have not yet transferred the colonists inside the evac.