Actually, move EVERYTHING in your FS2 folder other than root_fs2.vp, smarty_fs2.vp, sparky_fs2.vp, sparky_hi_fs2.vp, stu_fs2.vp, tango1_fs2.vp, tango2_fs2.vp, tango3_fs2.vp, warble_fs2.vp, and the fs2.exe, FRED2.exe, and Freespace2.exe, as well as any other executables if you've got FSO installed, into a folder named backup. Then create a new data folder, and copy the backup/data/players folder to data/players. That will effectively uninstall everything. Then re-install the port into the root directory (if FS2 retail) or a port/ directory (if FSO, so you can use -mod port to play the port missions). You need to clean extra crap out of your root directory pronto, because that's a sure-fire way to make a mess of things.
There's no point in replicating retail data though, as a base FS2 install is on the order of Gigabytes. Keep it simple.