Use this file if you want. The shuttles in the defaultcore have shields, mines and greater hull str. Note I did this by changing the class of ship from SH to FF if I remember. That way you can load out the shuttle the same as a ship. However I didn't give then photons though it could be done.
Please note this is a MOD. If you only want the improved shuttles. Then unzip this to somewhere besides your SFC3 folder.
Then find the shuttle entries in defaultcore and defaultloadout. Then cut each line seperate and paste them into the original game files. Making sure to delete the defaualt shuttle entries 1st. Always back up the original files 1st. You need to do this for each race's shuttle.
btw WINRAR is available here
http://www.rarlab.com/ There is a free trial period. You need it to unzip .rar files.
mod file