Yes, the crankshaft might be misaligned, and the main bearings will almost surely be the wrong size (unless the crank case has the same bearing number(s)). You'd also need new rod bolts (they elongate with the initial tightening and can't be reliably reused), new rings (it's improbable that the old ones will bed into the new cylinders), apart from the cams and timing parts there's not much you could just swap on an engine like this.
If you're considering opening the engine (and assuming you got all the tools needed, especially the torque wrenches), it'd be easiest and cheapest to just take the lower case half to a welder, this way you don't even have to remove the crankshaft or the pistons.