You can read about the 1986 to 2008 differences in the 3.0l Vulcan engine here:
https://www.therangerstation.com/tech/ford-3-0l-build/
You will need to swap upper and lower intakes with injectors and sensors, so the 2000 engine wiring and fuel system connections are plug and play
Also your 2000 Cam synchro/sensor needs to be swapped over to the 1995 block
The flex fuel vs gas only head chamber difference doesn't really matter, people have swapped these around for years with no noticeable differences
Both, for sure, run fine on gas only, if that's what you have, so the VIN "U" or "V" won't matter, as long as you swap intakes and injectors
Do put a note in engine bay that its a 1995 3.0l, just in case it ever needs a rebuild, as you will read in above article, there were several internal differences for parts
If the 3.0l Vulcan is from a Car then you also need to change head gaskets