Looks to me like you're not using PR10. You don't have to use the pce.ini to point the drive with the new PR10; you can select the daemon or real cd-rom drive from the menu making it easy. You're still using an old version of the emulator, which is usually due to fans having a pirated key, and it not working with the latest version. But let's not make assumptions here. Anyway, in a nutshell, this is what you need to try:
1) Download this,
http://www.magicengine.com/files/me100-english-pr10.zip and extract to some folder.
2) Download this,
http://rigg.servegame.com/software/SYSCARDS.rar and extract it in the same folder where you extract PR10. The 3 files inside this rar should be in the same folder as pce.exe.
3) Run pce.exe.
4) Select Boot CD.
5) It'll show you the drives, and if it detects a valid PCE CD, it'll say "PCE CD." Since you fixed the ISO/WAV/CUE file set with TocFixer, you should see it. Anyway, don't select the drive just yet. Click that arrow at the bottom you'll see. Then a bigger list of choices will appear; select SYSTEM CARD 3.0 and NOT the MAGIC SYSTEM CARD 3.0. When you do that, it'll show that card as selected.
6) Now go back up and select one of the drives where you saw that "PCE CD." You'll be taken to the system card menu, and when you press whatever key or joystick button is assigned as the "RUN", the game will begin. Usually the Enter key.