I was sort of surprised at how difficult of a time I was having getting just a basic disassembly / reassembly process going. After looking through a few of the commonly suggested toolchains, I settled on ca65 as it seems mature and has reasonable integration points with mesen. Plus I think Disch's FF disassembly has a pretty nice organizational template to go off of with respect to structuring the code in 'banks', building a ld65 memory map config file and disassembly labeling info file. (Shoutout to Disch for sharing that, by the way. That clearly took a huge amount of work and is a very cool contribution to the community!)
So, It looks like I'm going to need to bang out a few python scripts to get to the point where getting from rom w/ CDL file to reassemble-able source is a reliable, repeatable process. All I'm looking to produce is a set of source files with auto-generated labels and asset blobs replicated as bytes/bins, to be used as a starting point for labeling and stepping through code in a debugger. It looks like a bunch of people have cobbled together parts of this, but there's not much out there that isn't quite specific to the game they were hacking on at the time.
I just wanted to drop a post here to make sure I haven't missed anything out there that could save me some time before I dump a couple weeks into this. Please reply and let me know if I did! Cheers and beers.
(Appendix: Here are a few of the links I read through to gather info for this post)
one of the most interesting, although I'm not trying to get get too deep into "smart" disassembly, just baseline 'reasseble-able' code -> http://www.romhacking.net/forum/index.php?topic=29943.0