My favorite way of checking the code version is to get the MS-II code download program, which also works with Megasquirt-I. Install it, connect it to a powered up Megasquirt, and set it to your COM port number and a COM speed of 9600. Then go to File -> Read Signature. It will tell you what code version you have.
Note that some codes share signatures - for example, 029q through 029v and several experimental versions through 029x all have the same signature. However, as long as the signature is the same, they use the same INI file.