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The CHR and PRG ROMs have different pinouts even on US/euro NES carts, which I have never ever been able to figure out. Only thing I can think of is it was done to make REing difficult or something.
I always found myself in europe to have the same boards and pinouts as in US carts. According to bootgod's database, weird boards like SL1ROM or so only exist in US, never in Europe. Same goes for 3rd party boards such as NES-BTR or the Acclaim or Konami boards.
I'm not exactly sure, but I guess Famicom carts made by Nintendo are like the NES carts by Nintendo, they have their pinouts shuffled in the same way. I currently only have one FC cart so it's hard for me to say a rule based on this.
And I think most non-Nintendo carts uses standard (JEDEC) pinouts because they couldn't afford making special custom made maskrom, altough Konami or Namco could probably have afforded that if they really wanted.
The puropse may have something to do with reverse engineering, but also they could make smaller chips for 128kb (28 pins instead of 32) by routine /OE and /CE to the same pin. Also Wizard & Warriors II cartridges uses a pin for a positive CE in order to avoid bus conflicts, which couldn't be done without extra logic on a JEDEC pinout.
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(Also the NES cart edge is on a 2.5mm spacing, instead of .1" which is 2.54mm... I also suspect this was done on purpose to make american made carts unreliable if they used the .1" spacing)
Yes I've figured that out and I almost was gotten. After multiplying the spacing by the amount of pins I got a large error tough. I had to use a big zoomer (is that how is it called in english) to figure the truth.