If both engines are standard outputs the Vp44 fuel pumps will interchange without any physical or performance issues.
The Crankshaft on your 99 has a tone wheel which is monitored by a sensor. The 2002 only reads the Cam position sensor. Thats what you need to figure out.
You might want to swap cranks and cams and you should be good to go. If you want to retain the old ECM.
Thats my 2 cents.
There are people here who have encountered your same issue, hopefully they speak up!