Any 4.6 short block will bolt in, but if it is a bosch motor you have to swap over the senor plate welded on the back.
If it is a long block, a bosch block will work with a GEMS front cover and the sensor plate (make sure to find one withou air injection or plug the holes in the head).
If it were me, I would find any short block, recondition my existing heads, and fit a new cam, lifters, etc.
A full motor, I would stick with a GEMS motor.
Note, you will have to figure out what to do about the ECU. ECR has access to chips/tuning. The stock one will work but you will not see all the power increase you could.
*not legal advice*