All the mid 80s thru mid 90s TRX/ATC/CR/250/500 intakes and reeds use the same bolt patterns. They also use the "power" bend in the intake. If you can find the early(78/79) Elsinore cr250 intakes, they are a straight boot design and will hold a 39MM carb easily. I have run several CR250 4 petal reeds and they are the best of the factory stuff, IMHO.
You can also drop your stock intake and filter boot into a pot of boiling water for a few minutes and it will fit a larger carb easily too. Never done it to a fl400, just 350 stuff.
Hope that is what you were asking.