Installed the EJK Fuel Injection Controller, do you think this is causing the issue?
That might be a good place to start.
Agreed.
I took some time to look through that controller product instructions and FAQs. It's completely inadequate for your needs, and I'll explain why in a second. So, just take a few minutes to remove the body panels, and just uninstall the thing and restore your injector harnesses back to the stock configuration. Ride around for 40 to 50 miles to allow the ECM to adjust back to normal and I believe your engine problems will correct themselves.
Please understand that I'm not criticizing your decision or the product. But here's the thing. Your Spyder runs the exhaust through a 3-way catalytic convertor. Because of this, the Air-Fuel Ratio (AFR) needs to be tightly controlled. This is done by means of a feedback loop from the O2 sensors back to the ECM. This is called Closed Loop operation. The AFR is tweaked as needed through the use of short term and long term fuel trims, controlled by the ECM. Long term fuel trim values have a map of their own and are stored in memory. At higher power levels and throttle positions, the ECM switches to Open-Loop operation, where it meters fuel based on the mapping without O2 sensor feedback. Google all this.
So…your EJK unit does nothing to intercept, modify, or bypass the O2 sensor feedback in close loop operation. Nor does it even know throttle position. There is a reference to O2 sensor bypasses as an optional piece of equipment, but nothing anywhere on the site about how to obtain or installed them. Regardless, unless you remove the Cat, trying to enrichen the AFR with a controller will ruin the Cat and make it run even hotter than it is already. And without spoofing the O2 sensor signal to the ECM, the ECM is just going to try to undo everything the controller is trying to do. So yes, the controller and ECM are in fact fighting each other. I'm actually surprised you're not getting a check engine light and codes.
So, if you really want to add a controller to the Spyder, know why you're doing it. Take some time to train up on closed loop and open loop operation, short and long term fuel trims, and a basic concept of fuel mapping. The only product I know of that is satisfactory is the Power Commander. If you want to get maximum horsepower, then you need to tune for maximum horsepower, not tune to AFR. I think you'll be just as happy sticking with the Yoshi, keeping the Cat on, and eliminating the EJK.