Definitely the best option IMHO and with all the symptoms you now mention I would say 99% sure that all your issues are engine related
Do yourself a favour and, unless you know it is OK for sure, do a compression check on the $300 engine.
If that is OK I would only change the engine at first.
I would also suggest pulling the injectors and getting them serviced.
Those first generation ECU's were very reliable, I wouldn't change one unless I was sure it was knackered.