Having an issue where my R53 will consistently hit limp mode upon acceleration at operating temperature.

I see the EML and SES lights flashing momentarily, then continue to flash if I hit limp mode again. The wiper fluid light also flashes.

I’ve checked the blow off valve and I changed my spark plugs because they were black. My current thoughts are ECU issue or maybe the harmonic balancer? I thought the harmonic balancer would throw a trouble code though?

 

A failing harmonic balancer / crank pulley unfortunately will not show up as a fault with a scanner (at least none of the OBDII readers I've used).
Check your crank pulley. If it is the factory rubber core - the rubber center maybe starting to come apart and may cause your belt to be slipping.
Check and clean your coil pack terminals. You may want to spray carb cleaner and swab the inside of the rubber spark plug boots as oil, dirt an corrosion may be present.
It also maybe likely that an injector is clogged. Try an injector cleaning additive.
Listen for the fuel pump when turning the key to the second position. Fuel pump maybe starting to fail. You can pull the inter cooler off and check the fuel pressure at the rail/schrader valve with a pressure gauge - it should be around 45 - 55psi.
Try to read codes again with your scanner. Sometimes the fault will not show up immediately after the limp mode occurrence (e.g: DME P302 - misfire #2)

A couple of days ago my Mini ran fine. I decided after 20k+mi, I decided to change the plugs as routine maintenance..
The exact same issue as you describe occurred after stomping the pedal in 2nd . The car sputtered at 5k rpms , the SES, EML, DSC, ABS lights illuminated and went into Limp mode.
Scanned with my Foxwell 510 which turned up no codes. Mini ran/drove fine after shutting down and restarting (as long as I didn't stomp the pedal) - but the SES remained lit.
Upon investigating = The coil pack appeared fine, wires are NGK w/20kmi, plugs are new w/less than 50mi. I cleaned the coil pack terminals (320grit sandpaper) and a bit of dialectic grease.
Cleaned and swabbed the inside sparkplug boots. Surprisingly I discovered more oil residue than I'd expected. I also added a 8oz of Berryman B-12 chemtool fuel system cleaner to 1/2 tank of fuel.
My issue was resolve. The car runs great and acceleration is responsive.

Interestingly - When I re-scanned with my Foxwell 510 the original fault code popped up = " DME: Misfiring detected - cylinder 2 "

Sorry for the long reply. Just from my recent experience.
Good luck. Let us know what you find.