According to your log, you are loading the bin file:
[INFO] Using content: D:\games\PC Engine\selected_roms\ys1-2 from ia\Ys Book I & II [U][CD][TGXCD1002][Falcom][1990][PCE].BIN.
I tried the *.cue and everything looks good:
[INFO] Using content: E:\Roms\NEC - PC Engine CD - TurboGrafx-CD\Ys Book I & II (USA).cue.
I tested the redump verified cd:
Ys Book I & II (USA)
crc32 name
17623548 Ys Book I & II (USA) (Track 01).bin
8e029ac2 Ys Book I & II (USA) (Track 02).bin
caa50bd4 Ys Book I & II (USA) (Track 03).bin
271a0ab2 Ys Book I & II (USA) (Track 04).bin
d56fef33 Ys Book I & II (USA) (Track 05).bin
e591cddf Ys Book I & II (USA) (Track 06).bin
dfba60db Ys Book I & II (USA) (Track 07).bin
b5be0a75 Ys Book I & II (USA) (Track 08).bin
492a13cf Ys Book I & II (USA) (Track 09).bin
d11e92d5 Ys Book I & II (USA) (Track 10).bin
848ec05f Ys Book I & II (USA) (Track 11).bin
d14da754 Ys Book I & II (USA) (Track 12).bin
8b27ceba Ys Book I & II (USA) (Track 13).bin
c13b2b4a Ys Book I & II (USA) (Track 14).bin
b3c362b9 Ys Book I & II (USA) (Track 15).bin
3bbb5041 Ys Book I & II (USA) (Track 16).bin
be7cd2a9 Ys Book I & II (USA) (Track 17).bin
41d17cff Ys Book I & II (USA) (Track 18).bin
4acdee90 Ys Book I & II (USA) (Track 19).bin
794c6325 Ys Book I & II (USA) (Track 20).bin
62d5945d Ys Book I & II (USA) (Track 21).bin
bf176f7a Ys Book I & II (USA) (Track 22).bin
0aa01eee Ys Book I & II (USA) (Track 23).bin
fdfda849 Ys Book I & II (USA) (Track 24).bin
9b6801a8 Ys Book I & II (USA) (Track 25).bin
8518782d Ys Book I & II (USA) (Track 26).bin
9190d971 Ys Book I & II (USA) (Track 27).bin
e5f45a4c Ys Book I & II (USA) (Track 28).bin
6bff9f87 Ys Book I & II (USA) (Track 29).bin
e89d4251 Ys Book I & II (USA) (Track 30).bin
b610f3ff Ys Book I & II (USA) (Track 31).bin
ec1d08a5 Ys Book I & II (USA) (Track 32).bin
3d1dc160 Ys Book I & II (USA) (Track 33).bin
f2d52bec Ys Book I & II (USA) (Track 34).bin
d339b0f6 Ys Book I & II (USA) (Track 35).bin
f265c4df Ys Book I & II (USA) (Track 36).bin
4a818752 Ys Book I & II (USA) (Track 37).bin
3c97f070 Ys Book I & II (USA) (Track 38).bin
3ca46d90 Ys Book I & II (USA) (Track 39).bin
78bf9127 Ys Book I & II (USA) (Track 40).bin
9a79f72a Ys Book I & II (USA) (Track 41).bin
9b5d97c7 Ys Book I & II (USA) (Track 42).bin
9d41bf61 Ys Book I & II (USA) (Track 43).bin
b48cd34a Ys Book I & II (USA).cue
For the bios: you have to tell RA in Settings - Directory - System/BIOS
where to look for it.
On some systems the default setting is something like <Content dir>