Still doin' it, huh?

It's a real head-scratcher, all right. In searching the web, I see you've been on other forums looking for input, also with little help. The guy, vihn, who had a 2003 carbed motor, mentioned the CDI. I believe that he was referring not to your ECU but to a capacitive discharge ignition on his carbureted engine. So unfortunately, I would be suggesting that you not rule out having to replace the ECU itself. It seems that something that clocks is causing your problem, and the only thing that I know of that clocks would be the ECU. Of course, before dropping a whole wad of cash on a new unit, I would try like crazy to find a used ECU, or a real good friend who would let you swap the ECU out of his motor to try. Cheapest used ECU that I can find after a short search runs $435.
I do have one other idea, but with the
exact 35 second interval that you face, it's a long-shot ... but here goes. Your injected Yammie has two fuel pumps; a low pressure pump that feeds fuel to a vapor separator tank. Inside this little tank, sits your high pressure fuel pump, immersed in fuel. This is the pump that pressurizes the fuel rail for your fuel injectors. If the low pressure pump is weak or damaged, then every so often, the vapor separator tank may get low enough for just a second to cause the high pressure pump to cavitate, causing your hiccup. The low pressure pump's out put would be relative to RPM, as would the regulated fuel volume needed by the high pressure pump, so the hiccup interval might stay very close to the same at all RPMs. I'm not convinced at all by this suggestion.... like I said, a long-shot.
