I tried using gdibuilder, but when I tried to build the disc it said "disc image is too big for gd-rom, can't build"
When you're rebuilding a GDI, your goal is to only modify the part you want to change. Each disc of Shenmue 1 contains 6 tracks. Tracks 1 and 2 are the ones you can see if you put the original disc into a PC, Track 3 is part one of the file data. Tracks 4 and 5 are the AM2 and YS music jingles, then Track 6 is the rest of the file data.
You will want to first make a copy of the GDI somewhere else, so you can modify it without accidentally wrecking your original in case you mess up. Open the image in GD-ROM explorer, and under the "High Density" section, right click SHENMUE_DISC1 and use the only option in the right click menu to extract all of the disc data into a folder somewhere.
You'll also want to grab a copy of IP.BIN right above that, but don't put it into the folder where you extracted the data because it's outside that.
Once you have extracted the files and replaced the ones you want, in GDI Builder point it to the folder of data files you just extracted and modified. When it asks for IP.BIN, find the one you extracted. For CDA, provide the track 4 and 5 .raw files from your GDI that you copied. Set your output DIR to the place you copied the GDI to - GDIBuilder will overwrite Track 3 and Track 6 with new tracks that contain the files you modified. It also updates the .gdi file for you, if it's already in the output folder.
You shouldn't get a message that it's too big as long as you were only generating an image from the files on the disc originally (with your changes)
