I can only play for about 20 minutes at a time as this game is EXTREMELY stressful on the CD-ROM mechanics. Everything loads. It's like a CD System 2.0 game with only 64k of memory, very similar to Cosmic Fantasy 2 in the amount of loads. It needs to load every battle, every town, everything. And it does this A LOT. I am actually surprised that Super CD is required.
System 3.0 is required because this was done in HuC, first of all, and second of all, there's way more going on behind the scenes than CF2. CF2 lacks battle backgrounds, for starters... it also exploits the hell out of ADPCM RAM, which Mysterious Song only does for cutscenes since ADPCM samples are used for battle sound effects. And actually, the released version of Mysterious Song does WAY less loading than the initial prototypes, which spent a good 15 seconds loading data for battles when the program was self-contained. Splitting the program into map and battle systems reduced load time by over 90%. Load time was always an issue, and the way it works in the released version is the quickest way it could be done.
But as a result my CD drive will eventually "forget" to load until I nudge it. After a few times of that, I just turn it off. After it has cooled down it is fine again. This happens occasionally on other games, too. Always has since day one. But Mysterious Song really brings this issue out like no other game.
Your machine has a weak drive motor and overheats. The first Duo that BlueBMW sent me had the same problem; the second one does not. Seems to be a problem with Duo units especially. On the first Duo, it would work fine for about a half an hour and then start having reseek issues... after about 45 minutes, it was having reseek issues almost every time, and I had to let the thing cool down for awhile before playing again. On the second machine, I can play the game from beginning to end, using a CDR, with almost no reseeks.
EDIT: I think incorporating PSG music would have been much less stressful on the system.
Wouldn't have changed anything there, and would have been harder to pull off anyway. Squirrel wasn't up to par at the time, and memory was already tight so there was no way. Also, the original music is in module format, and would have lost a lot of quality converting it to PSG.