If you skip an IPBINHACK step - you're fool
In IP.BIN file stores all the main info about current CD. This file is necessarily.
Your problem is that you can't see 1st session of the cd where the Ip.BIN is located. It's not a problem - cause I have over 30 copied games and I made it selfbootable or simply copying already bootable game on other cd using an Ip.BIN file from SpaceChannel5. As I can understand it's no matter what ip.bin file you're using - cause echelon self-boot tool made all necessery changes of it. It works for me fine.
So, just copy all the files from the cd (from the 2nd session of it), remove read-only attribute. Then copy any ip.bin from any of your cd to the same directory. Follow the self-boot programm instructions as nothing happens.
I use this technique when I don't know how to back-up already self-boot games. Not all burning software can handle with multisession discs. Later I found DiskJuggler can.