Alright, sorry I was gone I had some unforeseen family matters I had to attend to. OK, 2 things, first off as to the editing the save file and turning of syncing with iTunes, it doesn't work, as this gentleman posted a hack (see bottom for link) that should have worked (loads of money and gems) but when you edit the library it changes everything, BUT the money and gems aren't added and your money goes to a negative 29k. That's why I'm trying to edit the mission rewards, or possible the make the price of a ship -100k coins and -100 gems (so it adds money to your total). Second, as for IDA pro, I am downloading it now, and hopefully I can locate the app files and edit them with it, but I'll post what I find using that.
Gentleman's Hack:
http://iosgods.com/topic/6411-naval-track-all-versions-2-cheats/?p=165821
UPDATE: Using IDA pro I was able to locate the apps directories, the only problem is I can't find where the values for buying ships are, or mission reward stats are. (not listed, I tried searching manually and then by searching the strings for words like coins, cost, reward and gem)