1999 ranger drive shaft

:confused:i pulled the driveshaft to have my 1999 ranger to tow.3.0 engine auto trans 2 wheel drive, i replaced the engine,the tranny worker fine before engine change now it makes a grinding noise when i accellerate hard, i looked in repair manual after the fix, it says to mark driveshaft before removing,is it possiable to hook the driveshaft up out of time ??how would i know if it is right?? thanks in advance, skip:confused: