You're comparing apples and oranges. Both are good motors, one is a high-revving, performance NA screamer. The other is a truck motor that has stacks of torque, is pretty bulletproof and has almost unlimited potential if you turbo it and do more work (have a look at some of the Peurto Rican drag cars running 8s, or maybe even 7s with them).
Yes, the 3S should bolt onto your crossmember, but that will save you max 5% of the work for the conversion. Basically don't choose your engine solely due to this.
What are your plans? What do you want the car to be? And how big a project do you want? Also there is probably a long list of things you should do to the car before jumping into an engine conversion.
Hen