Mednafen supports iso+wav+cue also. In other words, you could have stopped after converting the mp3s to wavs, and just used your valis1 (J).cue.
However, mednafen-rr and pcejin accept only bin+cue. Plus it's touchy that the cue only reference data and audio tracks and no other information. So do the following:
1) Throw away the bin file you made from the iso file.
2) Put the wavs with your iso file and mount them in Daemon with this cue:
FILE "Track No01.wav" WAVE
TRACK 01 AUDIO
INDEX 01 00:00:00
FILE "track02.iso" BINARY
TRACK 02 MODE1/2048
PREGAP 00:03:09
INDEX 01 00:00:00
FILE "Track No03.wav" WAVE
TRACK 03 AUDIO
PREGAP 00:02:00
INDEX 01 00:00:00
FILE "Track No04.wav" WAVE
TRACK 04 AUDIO
PREGAP 00:00:06
INDEX 01 00:00:00
FILE "Track No05.wav" WAVE
TRACK 05 AUDIO
PREGAP 00:00:07
INDEX 01 00:00:00
FILE "Track No06.wav" WAVE
TRACK 06 AUDIO
PREGAP 00:00:06
INDEX 01 00:00:00
FILE "Track No07.wav" WAVE
TRACK 07 AUDIO
PREGAP 00:00:06
INDEX 01 00:00:00
FILE "Track No08.wav" WAVE
TRACK 08 AUDIO
PREGAP 00:00:07
INDEX 01 00:00:00
FILE "Track No09.wav" WAVE
TRACK 09 AUDIO
PREGAP 00:00:05
INDEX 01 00:00:00
FILE "Track No10.wav" WAVE
TRACK 10 AUDIO
PREGAP 00:00:07
INDEX 01 00:00:00
FILE "Track No11.wav" WAVE
TRACK 11 AUDIO
PREGAP 00:00:05
INDEX 01 00:00:00
FILE "Track No12.wav" WAVE
TRACK 12 AUDIO
PREGAP 00:00:06
INDEX 01 00:00:00
FILE "Track No13.wav" WAVE
TRACK 13 AUDIO
PREGAP 00:00:08
INDEX 01 00:00:00
FILE "Track No14.wav" WAVE
TRACK 14 AUDIO
PREGAP 00:00:07
INDEX 01 00:00:00
FILE "Track No15.wav" WAVE
TRACK 15 AUDIO
PREGAP 00:00:04
INDEX 01 00:00:00
FILE "Track No16.wav" WAVE
TRACK 16 AUDIO
PREGAP 00:00:06
INDEX 01 00:00:00
FILE "Track No17.wav" WAVE
TRACK 17 AUDIO
PREGAP 00:00:05
INDEX 01 00:00:00
FILE "Track No18.wav" WAVE
TRACK 18 AUDIO
PREGAP 00:00:07
INDEX 01 00:00:00
FILE "Track No19.wav" WAVE
TRACK 19 AUDIO
PREGAP 00:00:06
INDEX 01 00:00:00
FILE "Track No20.wav" WAVE
TRACK 20 AUDIO
PREGAP 00:00:06
INDEX 01 00:00:00
FILE "Track No21.wav" WAVE
TRACK 21 AUDIO
PREGAP 00:00:05
INDEX 01 00:00:00
FILE "Track No22.wav" WAVE
TRACK 22 AUDIO
PREGAP 00:00:03
INDEX 01 00:00:00
FILE "Track No23.wav" WAVE
TRACK 23 AUDIO
PREGAP 00:00:07
INDEX 01 00:00:00
FILE "Track No24.wav" WAVE
TRACK 24 AUDIO
PREGAP 00:00:04
INDEX 01 00:00:00
FILE "Track No25.wav" WAVE
TRACK 25 AUDIO
PREGAP 00:00:05
INDEX 01 00:00:00
FILE "Track No26.wav" WAVE
TRACK 26 AUDIO
PREGAP 00:00:07
INDEX 01 00:00:00
FILE "Track No27.wav" WAVE
TRACK 27 AUDIO
PREGAP 00:00:05
INDEX 01 00:00:00
FILE "Track No28.wav" WAVE
TRACK 28 AUDIO
PREGAP 00:00:07
INDEX 01 00:00:00
FILE "Track No29.wav" WAVE
TRACK 29 AUDIO
PREGAP 00:00:08
INDEX 01 00:00:00
3)Use a dumping program to convert the mounted virtual CD to bin+cue. I used ImgBurn myself.
4) You should end up with a big (>500 MB) bin file and a cue that looks something like this:
FILE "Valis.bin" BINARY
TRACK 01 AUDIO
INDEX 01 00:00:00
TRACK 02 MODE1/2352
PREGAP 00:02:00
INDEX 00 00:44:53
INDEX 01 00:45:63
TRACK 03 AUDIO
PREGAP 00:02:00
INDEX 01 03:38:42
TRACK 04 AUDIO
INDEX 00 05:38:61
INDEX 01 05:38:68
TRACK 05 AUDIO
INDEX 00 07:42:16
INDEX 01 07:42:24
TRACK 06 AUDIO
INDEX 00 09:43:74
INDEX 01 09:44:06
TRACK 07 AUDIO
INDEX 00 11:45:20
INDEX 01 11:45:27
TRACK 08 AUDIO
INDEX 00 13:47:70
INDEX 01 13:48:03
TRACK 09 AUDIO
INDEX 00 15:49:60
INDEX 01 15:49:66
TRACK 10 AUDIO
INDEX 00 17:52:34
INDEX 01 17:52:42
TRACK 11 AUDIO
INDEX 00 18:12:67
INDEX 01 18:12:73
TRACK 12 AUDIO
INDEX 00 18:38:02
INDEX 01 18:38:09
TRACK 13 AUDIO
INDEX 00 19:03:60
INDEX 01 19:03:69
TRACK 14 AUDIO
INDEX 00 19:34:06
INDEX 01 19:34:14
TRACK 15 AUDIO
INDEX 00 19:48:09
INDEX 01 19:48:14
TRACK 16 AUDIO
INDEX 00 20:12:58
INDEX 01 20:12:65
TRACK 17 AUDIO
INDEX 00 21:43:66
INDEX 01 21:43:72
TRACK 18 AUDIO
INDEX 00 23:17:48
INDEX 01 23:17:56
TRACK 19 AUDIO
INDEX 00 25:53:57
INDEX 01 25:53:64
TRACK 20 AUDIO
INDEX 00 27:31:54
INDEX 01 27:31:61
TRACK 21 AUDIO
INDEX 00 28:51:59
INDEX 01 28:51:65
TRACK 22 AUDIO
INDEX 00 30:02:01
INDEX 01 30:02:05
TRACK 23 AUDIO
INDEX 00 35:18:16
INDEX 01 35:18:24
TRACK 24 AUDIO
INDEX 00 42:00:66
INDEX 01 42:00:71
TRACK 25 AUDIO
INDEX 00 45:03:55
INDEX 01 45:03:61
TRACK 26 AUDIO
INDEX 00 48:23:36
INDEX 01 48:23:44
TRACK 27 AUDIO
INDEX 00 48:57:22
INDEX 01 48:57:28
TRACK 28 AUDIO
INDEX 00 49:43:17
INDEX 01 49:43:25
TRACK 29 AUDIO
INDEX 00 49:56:22
INDEX 01 49:56:31
5) Now load pcejin (or mednafen-rr) and point it to that cue file. It should work now if you have your bios set up right.