They don't need any flashing to change gear ratios. The tone wheel is on the ring gear and is not affected by gear changes, it still turns the same rpm as the tire no matter what gear is in it. However changing tire diameter will change your speedometer. The actual rear end may have different number of tone wheel teeth but I have never counted them and never been asked by my mac, snap-on scanners or the old DRBIII what diff is in one when programing the "pinion factor" as they call it so I would suspect they are all the same.

Are you sure you got a dana in it? I have two of those vans and they both have 9.25 rear ends in em. Also both of them have 3.92 gears, ones an 01 and ones a 92.