Question 1: Is the motor the same on the 1300 non-ABS, ABS, and PA? YES!
Question 2: Is the ECU interchangeable? NO!!
Let's get into the nuts and bolts of your question. Dropping this engine is no easy task. For me I can do it in 3 days. For your very first time it will take 60+ labor hours to complete. But let's go back to question zero: Why are you swapping the motor?? These things are overengineered. If your engine is truly toast [ie ran 10k miles on no oil] then you will need to start shopping the auto auctions.
STUDY. THE. MANUAL.
Let's get into the harness question. I restored a bike recently the owner wanted to convert it into an escort bike. He paid the man to change it over and [insert shock] IT DIDN'T WORK!! He took it to a catch all motorcycle deal that charged him a couple grand to not solve the problem. The harness was butchered by whoever removed it from the salvage bike and it was obnoxious to fix. Let's get into the ECU: THE L01 AND R21 ARE NOT INTERCHANGABLE!! What is on your bike is what you've got. The police bikes run different alternators with higher amp loads that the civies don't have. [130 vs 145 amps]
VERY IMPORTANT: Honda has published that the 31100-MCS-003 civilian alternator CAN BE REPLACED with the 31100-MCS-013 PA Alternator without any mods to the wiring harness!!!
When you're done with the swap, do not dispose of the engine. It can be torn down and repaired. KEEP IT. These blocks are getting harder to source. Fixing it for a couple hundred is cheaper than sourcing an unknown engine.