You'd have to remove the soldered-on RAM at U25 and install an IC socket, unless someone has already done that. After that as long as you're replacing with the same type of nvram module (should be a 6116) there's nothing else needed. If replacing a 6116 with a 6264 chip (on later boards that allow for 28-pin chips) you'd have an additional jumper change. Battery holder can stay or leave, if the battery terminals have corrosion it's best to get it off of the board if you're working on the board anyway.

i thought there was a jumper i changed too...

Only if upgrading to a 6264. I believe all Williams Sys11 came with 6116 RAM installed from the factory, so if you're replacing that with a 6116 NVRAM no jumper changes are needed. The only time a jumper change needs to happen is if switching to a different type of RAM than what's currently installed in the board.

Once the NVRAM is installed and working you can then reset to factory defaults (see the manual). Then it's a matter of setting free play, high score levels & other adjustments as you wish. As far as any other hardware changes, as long as you're replacing "like-with-like" (ie. 6116 RAM comes out, 6116 NVRAM goes in) then there's nothing else needed there.

Also the traces are very very delicate on system 11 boards and the boards are unavailable and can't be replaced so unless your very good at board work I wouldn't attempt it.

My U25 says the RAM is a 5516.

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TC5516 is Toshibas part number for a 6116.