As I posted on my Twitter... the issue was that the Chinese handheld clone I use (a 'PocketGame') was not compatible with Ecco Jr or Tides of Time, leading me to believe I'd made an error.
I measured all the voltages for all three games, and they were correct.
Then I desoldered the banking chips and manually jumpered the games, again, the same result.
I fixed my hack of Gens to support the new scheme - the code all worked fine (on the plus side I fixed some sprite corruption I'd seen - the VDP DMA didn't take banking into account.)
I assumed bad burn and burnt new EPROMs. This time I tried the first one in my test cart, and when Ecco Jr again failed, I got very suspicious. I went and got the original PCB for Ecco Jr, which I had thought defective (and was the catalyst for me to do all this...) It didn't work in the handheld.
So, I went and got my real Genesis. Then I needed to find a screen that took S-Video, since my Genesis is modded (I /like/ S-Video, damn it!) Turns out I only own one, but that was enough. And Ecco Jr worked fine there. Tried my test cart, worked.
Since I had new EPROMs burned, I repaired the first cart AND finished a second. I then put Ecco Jr in a new shell (I had destroyed the original label by covering it with my 3-way label, so that's disappointing. Hopefully I can download a nice copy of the label and reprint it). Both carts are working fine... and I am done for the moment.
If anyone wants a Thunder Force or an Ecco, I have three TF and 1 Ecco spare... they're $30 plus shipping to cover my costs. I can also make Jaguar repros since I have some spare PCBs there, but those will cost a bit more (because Jaguar) and you need to provide your own shells.