Allen,
You shouldn't have any, so long as you use all the sensors and accessories
from the old engine. The 1993 was an OBDII and the 1999 is an OBDIII, so
there may by minute changes (for example the egr is external on the 93 and
internal on the 99). If I were you I'd strip the 1999 to the long block, then
bolt on everything from the 1993 engine to the 1999. You shouldn't run into
any problems like that.
If I were you I'd take the opportunity to adjust the bands on the
transmission and replace the O2 sensor while you got that gaping hole in the
engine compartment.
-Austin
Vipertruck
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