How about the best of both worlds? Leave the interface as-is with the default 10 and 3, but provide a check box that would direct the program to ignore those tones stored in the config file, and instead use an external file. Users who don't need more than the default amount can continue to use the interface, and those that need more would instead have to use an external file.
The trouble with adding more fields to the interface is, at what number do you stop adding additional fields? What if someone wants to set the program up with 500 tones? Might seem like a lot to us, but maybe not to that person. Even if the interface were scrollable, it still doesn't solve the question of how many fields does he add. With an external file, it would theoretically provide infinite tone set.
I'm running the program on an older computer, which doesn't really like running more than one instance of the program simultaneously. I understand that on a faster machine I could run more than one instance without much trouble, but I would hope you'd keep those of us that might have a dedicated older machine doing this work in mind.
Lastly, while I think it would be easier to maintain a spreadsheet file of the additional tones, I'm not sure if that gives the best compatibility for all users that a .txt file would. I would echo jpryor's request that if you do decide to go with a .txt file, have it csv with each entry on its own line.
1500.0,850.0,Tone Set 1,tone1@domain.com
2000.0,1000.0,Tone Set 2,tone2@domain.com
etc.