I personally would focus on the coil / no spark issue first, then go from there. When you removed the plug and smelled the plug and smelt gas , since the bike has not run in a while it would lead me in the direction that the injectors are ok seeing they and the emc have been replaced.

 

Your system relay is what allows power for the first few seconds to both the coil and fuel pump when you turn the ignition on before it settles into a standby state waiting for the starter to be hit at which time it re-energises and allows the fuel pump to run constantly and for the coil to allow sparking.
As I mentioned above, to see if you have a spark, you must have plugs in the head and use a spare plug or inline spark tester or you will never see a spark at the plug caps even if the ignition system is fine.
The fact that the fuel pump isn't energising at ignition on would have me swapping out the system relay with the start relay to begin with and take things from there.
Put your finger on the system relay and see if you feel it click when you turn the ignition on.

 

Is the system throwing any diagnostic codes? If any of these systems are failing, I would think that there would be a recorded code.

You don't have to pull the plugs if you want to test spark. Another name for an "spark tester" is called an "inductive timing light". If you know anyone who works on older vehicles, they'll have one of these. Hook it up to either wire, turn the engine over, if you see the strobe, then you've got spark.

Since the shop put in a new ECM, did they flash it? You can buy these things new, but they come blank. They still need to be flashed.

Also, do you have a security module? If the TSSM has gone bad, that will keep the bike from running.

 

So the mechs at the HD shop couldnt figure it out and just gave up on it? I hope you get it figured out.

 

2007s are notorious for corrosion issues in the fuse block/relay area. Be sure and pull the relays and clean the contacts just like with the fuses.

 

Try swapping the relays. If it goes from not starting to not cranking you will know it's a relay.

My 2007 1200C was shutting off intermittently and it turned out to be in the system relay. Contacts were already clean and greased. I found a generic replacement at O'Reily auto parts and replaced both of them.

https://www.hdforums.com/forum/sport...reference.html