Glad to here you have MAG's support to do the updates. Moving this to public development then.
First thing before releasing anything is to put the missions up for beta testing and get some feedback. There are probably more bugs then what you have found and of course the possibility you created some new ones.
As for when release time comes I'm not sure what the best way to proceed would be. One of the bad habit carry overs from the original install was placing mission/campaign VPs right in the root TBP directory. Updating the VP and put it back there would result in not being able to play with the old 3.6.9 builds which is something we try to avoid. Believe it or not there are still people out there using the old 3.6.9 DirectX builds. Another possibility would be to just pack the missions in a MAG.VP and put them in Zathras. As fixes they qualify for being located there. The third option is creating a mod directory for the campaigns and putting the fixed vp's there. I guess it will all come down to how many missions are changed.