Well, salvaging the board design is not a big issue, it's easy to lay out something else. In any case, after putting the other components on, I've discovered that I'll really need more bulk capacitance for the input voltage regulator, I had to hang an external cap on to get it all working with a load while charging.
On the good side, for what I was targeting, it works perfectly right now. If you replace your TMCC 9V battery with this, it will ride out an interruption of power for 8-10 seconds supplying around 125ma, that's more than most RailSounds boards are drawing. Since while it's charging, the battery is not being called on to deliver any power, the input regulator current draw is not an issue in TMCC use. I'm kind of torture testing it with a continuous load, so the input regulator is working all the time. In the real world, the input regulator will be idling 99% of the time, and only be needed when you have a power interruption.
I'm flipping a coin as to whether I should add capacitance or just let it ride. I'm tempted to add a spot for a couple additional 150uf caps. They can be optional parts if you're doing something that draws continuous power from the battery. That would be easy and not compromise the rest of the design.
The bottom line is it's doing what was intended! 
Thanks for spotting the obvious error, that's what I get for making an assumption. 
I'd say we smashed right through the size targets as well, much smaller than the 9V battery in all dimensions. Truthfully, I'll fit in places that the 9V battery won't.
