You know, I had a similar symptom when I installed a Starcom intercom system.
You might well say, "That's got NOTHING to do with the engine," and I would have agreed with you.
BUT- I took the power for the unit off a wire at the back of the bike near the tail lights that was only live when the ignition was on so I thought I just had a light wire. It was nicely accessible, being outside the main loom.
When I ran the engine it was very unwilling to idle, and when I rode off it was completely gutless. I was completely bushed as to what I could have done, and went looking for crushed vac lines etc where I'd run CB unit cables under the fuel tank.
As soon as I unpluged the power to the Starcom, the engine came to life.
I still don't know what the wire is (can anyone help?) but I found myself another power wire.
So you didn't happen to tap power off a wire attached to the rear LH side frame recently, did you?