Yes, I don't see any problem with using a newer long block.
In '99 I think they did a redesign and changed to longer head bolts, so keep track of the model year of the engine, because if you get parts for a '94 3.0l it might not be the same for an '04.
Just as a heads up I think the '03-'06 3.0ls had valve seat issues, TSB here:
http://ww2.justanswer.com/uploads/s420/2010-10-11_155436_04_rANGER_tsb05-26-03.pdf/
On the 4.0l OHV's they redesigned the oil pan gasket 3 or 4 times, and they are not interchangable, not sure on the 3.0l, but easy to check part numbers.
Check parts numbers to see if intakes line up, they should.
I have not done a 10+ year swap but from what I see I don't think there would be a problem if you are just using the long block.
If you can get the VIN number of the vehicle the 3.0l comes from it can help in IDing the exact model, as they change versions mid year some times.
This thread has some good info for 3.0l up to 2003:
http://www.therangerstation.com/tech_library/3_0-build.html
The FWD(front wheel drive) refers to vehicles like the Taurus/Sable not 4WD, these 3.0l engine were transverse mounted, but the block and heads are the same as RWD or 4WD Rangers, but because the coolant flowed out of the back of the engine to the rad the head gaskets were different to make the flow from front to back, head gaskets can be changed to Ranger gaskets and those 3.0ls can also be used.
Also price out Long Block exchange, rebuilt 3.0l long block price might not be that much more and you are not buying a "pig in a poke", used engines are tested and usually guarantied but........labor to remove and reinstall is not, lol.