There are a couple ways of doing this which will be much easier on you. First of all, are you using CDWav to track your wav file? If not, def download this freeware. Before opening the file in CDWav, save your file using the format of the desired final name. i.e-
phish2004-01-01d1t. By saving the file this way, CDWav will automatically name all of your files correctly. It just adds 01, 02, 03, etc after the "t" of the file name mentioned above. When you are done splitting the tracks, click save. You will have the option of choosing your output file type. Here you could set it to FLAC, and it will save all your tracked wavs as tracked FLACs. I myself first save them as wavs, then convert to flac by dropping all the tracked wavs into the Flac Frontend. This way I have wavs to burn to disc, and FLACs for uploading to LMA, BT, etc.
Let me know if this makes sense, but yeah, there is a much easier way of doing this.
Jesse