Is it possible to add the music and sound effect files from the FDS ROMs of Zelda I, Zelda II, Metroid, Kid Icarus, Castlevania II and Doki Doki Panic (Super Mario Bros. 2) to their NES ROM counterparts and get them to work on them?
For NES Castlevania II and III, Metroid and Kid Icarus, the localization teams re-composed the tracks entirely. Overall the quality was a mixed bag, with some tracks turning out better and some turning out worse. These are probably your main reference points for "Transferring" the songs of FDS games with those extra sound channels. You are not gonna be able to replicate the proper sound of the extra sound channels (Or at the very least, I've not seen one attempt to replicate a FDS sound purely into a base Famicom/NES sound.) and it would take VERY clever music recomposition to recreate any songs and tricking one's ear into feeling like no audio data was lost.
Zelda II and Doki Doki Panic might be interesting for the fact that their "different" music is still mostly base Famicom/NES sound, but generally people prefer the redone tracks for the localization on both.
I'd almost think it would be easier just to hack AST to be one ROM and function more like ALTTP.
Two big things get in the way of simply combining the AST ROMs into one:
1) Sheer size
2) The episodic structure pretty much enforces each episode to be standalone, which would null any point of combining the ROMs. You can't simply go from Level 2 to Level 3 or from 4 or 5 or from 6 to 7, which is what people would -actually- want from the combined set, even if it's not explicitly voiced out.
I would argue that it'd be easier to hack LttP and simply re-interpret the gameplay so that the game clock and episodic structure are non-factors, and the plot rewritten just enough so that there's no enforced breaks or waits.
Also, the game has 8 stone tablets. That ruins the easy option of just doing a graphics edit of the crystals or pendants.
Hogwash. That's 8 stone tablets for 8 TOTAL dungeons, compared to LttP's 12. Just edit both the crystals and pendants into tablets. There's no other end-of-dungeon items to get in AST.