No problem. Make sure you do all the maintenance/tune up things you can while the engine is out of the car.

Timing belt
Water pump
Clutch/flywheel
PCV valve
Sparkplugs/wires
Distributor cap/rotor

I wouldn't say that any of these are absolutely necessary, but some of them are much easier to do while the engine is out..especially the first few. You can also never be too sure about a used engine that's been sitting for 5-10 years.

Search the archives and you'll find everything you need to get these things, as well as the swap, done.