I haven't been able to focus on this too much over the past few months, but I have a bit of time now and am back to making progress. The biggest thing I've done is port the core over to C++. The C# core was just way too slow, and was falling under 60 fps even in simple cases. I expected I would have to do this so built the C# core to be conversion friendly from the start, but it still took a bit of effort. Converting to C++ and making a few basic optimizations about doubled the speed, and now I at least have a bit of headroom to work with. I expect more complicated scenes to still fall below 60 fps until I optimize a bit more, but that's a concern for further down the road once the rendering pipeline is finished.
Aside from that I made a bit of progress with rendering timing and open bus emulation, so I can get past the misc edge case timing test on the mGBA test suite:
I still plan to develop the rendering pipeline in C# as it's just much easier to bug fix in it, so for now both cores will be developed together. Sprites are the next thing to do.
EDIT: It now desyncs after the wrong warp. Lot's of crazy stuff is happening there, could be anything going wrong. Probably the new last boss of NES console verification outside of resets.