Single Player Prestige
To start the game with more Prestige funds, search for the sfc3 folder on your computer and open it. From here, open the folder Metaassets, then ServerProfiles, then singleplayer. In singleplayer, open the text file called Character, then find the lines that reads "// This is a character's starting prestige / [Create/0] / StartingPrestige = 200 / [Create/1] / StartingPrestige = 100 / [Create/2] / StartingPrestige = 50". The Create 0,1 and 2 lines designate Commander, Captain and Hard mode respectively. Change the StartingPrestige value to 999 999, save the file, then start a new game. You will begin with 999 999 Prestige.
Cheaper Items
To make bonus items cheaper, open the Program Files folder, then Activision, then SFC3, then Assets, then Common Settings. Within this folder, there are multiple .gf files. Open each and find the section that begins "[ComputerItemsF-COMPUTER-I] / Description = ''F-COMPUTER-I'' / Cost = 500 / Mass = 100". Change the cost value to whatever price you want. At the end of this section, the "Race = 'F'' value corresponds to the race the game is played as. For Federation, leave the value as "F". For Romulon, Borg or Klingon modes, change the value to "R", "B" or "K" respectively.
Federation Ship Cloaks
Search for the sfc3 folder, then open Assets, then Common Settings, then open the file named Bridge Items. In the section that reads "[CloakItems\R-CLOAK-V] / Description = ''R-CLOAK-V'' / Cost = 2500 / Mass = 50 / CloakRating = 500 / CloakCost = 10 / Health = 50 / Race = 'R'', change the Race value from "R" to "FR". This will enable you to buy the highest functioning Romulan cloak for any Federation ship from within the in-game Refit screen.
Choose Your Ship
Within the sfc3 folder, open Metaassets, then ServerProfiles, then open the text file named Character. In the sequence that reads "// Starting ships for players (sorted by RACE) / [StartingShips/0] / 0 = ''Norway'' / 1 = ''K'Vort'' / 2 = ''Falcon'' / 3 = ''Diamond'' ", each number value denotes the following campaign option: 0 = Federation, 1 = Klingon, 2 = Romulan, 3 = Borg. Replace the ship name for your campaign with a ship of your choosing, save the file, then relaunch your campaign to receive that ship.