'01 Lesabre engine into '96 Bonneville--Question

The guy at the junkyard said we only had to change the harmonic balancer and the oil pan for it to fit(I'm assuming the balancer was for belt alignment and ???--would that screw anything up?). Well, after swapping most of the brackets and accessories from the old to the new, it's in and it runs. Anybody done something similar before, with any tips, lessons learned, etc.? We're now modifying the vacuum system since they differ slightly, and there are a few mismatched plugs that need to be changed. One of which are the injector plugs. We put the old injectors on the new fuel rail, and it seems to work(it was 5:00 am at that point, just wanted it to run). I'm sure the new injectors are prefferable, and I'll likely get the right plugs and splice them in so I can use the new injectors eventually. Any issues with using the old ones in this manner in the mean-time? I don't know if there are any computer issues I need to worry about????? The bulk of the connectors were the same, and it fired right up. I'm wondering if it might not be a bad idea to get a scan tool and check it out, or will that tell me anything useful? Any tips, help, etc, would be much appreciated. A few friends have voiced concern that swapping the old harmonic balancer in place of the new might be a bad idea???? Could this cause problems?