ok I replaced the super cap with the one sold at arcadecomponents.com
Last night I could power down and switch games and the system settings would remain. It was on for a few hours before I powered down for the night. But this morning when I switched on, the system settings were default. Was my installation a failure or must the system be on much longer to charge the cap?
Guys. The super cap is not for saves!!! The pcb has a CR2032 battery for saves. The super cap is probably there just to ease the transition from on power to off (you guys remember the warning to hold the reset button on NES while powering off?). Lost settings = bad battery.
The cr2032 coin cell battery holds the cart settings, not the game assignment settings.
EX: If you unlock all the hidden characters in MvC2, the CR2023 helps save that info. But if you flip your game from verti to hori, then the super cap helps save that info.
Tyranix95 is correct. Yesterday I left it on all day and powered down at night. This morning I powered on and the system settings were still saved. This confirms I did need to have the system on longer for it to hold the save longer. The coin battery was removed the whole time. Two backup methods seems stupid.