Definatly buy the entire bike if possible, there will be many parts you may need if its your first time fitting a bike engine, bare this in mind if buying components individually, items that could be overlooked are the ECU and fuse/relay box, (should come with the loom but may not?) fuel pump and all fittings for location to new tank, switchgear could be usefull for adapting straight to dash or to new switches, all sensors relating to the engine such as possible ambient temp sensors which may be located remotely,dash clocks could be adapted to use as is and could be recalibrated to suit drivetrain used, exhaust and silencer as these can be expensive to buy if bought separate, another component essential on bike engines is the air intake system or Ram Air if fitted as if this is not present the ECU may need to be remapped with a power commander or similar product.
Just for example, there was a accident damaged ZX10 on Ebay recently, I enquired and could have the entire bike for £800 if I had it that week, thats a 186bhp next generation power unit for realistic money!
Its horses for courses really, plus if you buy the whole bike there will be a few parts that could be sold on if undamaged to recover some of the cost.
Chris.