Just plug the ECM in and run a test light between earth on the battery and the Yellow/Blue wire on the coil plug and try to start the bike the test light should go on and off.

 

the ecm is sending a ground pulse, to check for this pulse at the harness terminal, the test light has to be hooked up to the POSITIVE terminal of the battery, since the ecm is sending a ground signal. if you have it hooked up to the negative terminal, you wont see anything.
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Sorry I meant positive terminal as well.............brain freeze
It's just like the injectors and I know that

 

I get flashing light on the BE/O wire but none on the Y/BE wire. Where do I go from here?

 

ECM is bad - you checked that wire before and it is not grounded and Ωed out properly so ECM has developed a fault and needs to be replaced.

 

What are my options? Go with factory replacement or other? Is replacement something I can do myself?

 

Just my opinion but I prefer the OEM factory ECM rather than aftermarket.
You could buy a 2nd hand one of Ebay and do the marry it to your bike at home but you don't know the history of the ECM and what is on it.
Some diaganotic tools like the Centurion can now prep/format a ECM with the correct VIN on it for you.
Otherwise the only option is a dealer.

 

If I got a new ECM from Harley Davidson could I put it in myself or would I have to have them install?

 

New ECM needs to be programmed with VIN so they have to do it.

 

I checked with a couple of local dealerships. Looks like if the ECM has to be replaced it’s going to cost around $900 and the ECM is on backorder, should be available the end of next month. Looks like that's my best option?