
If you want to have all unlocks, you can use the cheats in the mod launcher.
On the settings tab, you'll see some settings. Enable the following:
Unlock All Rewards Unlock All Missions Starting Coins
Some mods have a Main=1 flag which makes them create their own save game files.
You can find these in Documents/My Games/Lucas' Simpsons Hit & Run Mod Launcher/Saved Games.
I'm not sure why your game would not load the saves even after playing without mods, could you list every mod and setting that you have ticked on the launcher?