How does P&L comes in?
Anyway see the pic below esp the pip cost column. Not sure if it is helpful.
You mentioned the 3 ps GBP/JPY EUR/JPY EUR/GBP.
So if you see GBP/JPY each pip would be worth 0.9 of what you see.
if you see EUR/JPY each pip would be worth 0.9 of what you see.
as for EUR/GBP each pip would be worth 1.76 of what you see.
So in excel you can just add an extra column e.g. "Actual GBP/JPY value" with value as =GBP/JPY_Col * 0.9.
PS.: The rates were captured at this point of writing. The numbers are just a rough gauge but should not vary too much too soon.