I'll join in with my thoughts.
Current draw from fans like the Love Jugs is unlikely to be a problem of any sort.
Except at very low speeds indeed, Love Jugs will produce much less cooling than the simple air flow due to the movement through the air and at speed there is more even cooling of the cylinders due to the cowl that the factory cooling kit includes. I was told by one of the engineers involved that the improved cooling at speed was a bit of a welcome surprise to them when they were developing the kit. Any cooling effect from a fan will be utterly overwhelmed by the wind rush by about 30mph or even less.
Skip fire is disabled when the cooling kit is fitted, you might want to re-enable it if you fit manually actuated fans in case of forgetting to switch them on in time. Presumably your ECU is unlocked so changes can be made.
The various oil cooler arrangements will certainly cool the oil but the engine is primarily directly air cooled by the fins on the cylinders so a reduction in oil temperature doesn't necessarily make a big difference to overall engine temperature. Some engines such as the original Suzuki GSXR bike engines were oil cooled but they had oil galleries similar to a water cooled engines water jacket around the cylinders specifically to give even cooling and they had enormous oil coolers to cope with the amount of heat generated.
I'll take a punt that the uneven running when hot for an extended period is more to do with something electrical. My suspicion would be on the the plug leads, the coil and possibly an out of adjustment throttle position sensor. The standard plug leads are not the best and are prone to breaking down particularly if they have been pinched by the bodywork or over zealous tie wrapping which leads to poor sparks. The coil generally isn't a problem on the M3W but a dodgy coil can give heat related misfires. The throttle position sensor is officially non adjustable according to S&S and needs the throttle body returned to them for calibration. In reality the adjustment screw is simply covered by a plug of silicone which can be unpicked, then it's a case of checking the voltage it gives on a closed throttle and adjusting the screw to give the correct figure. It would of course be more helpful if I could remember the correct voltage...apologies but I've never written it down but someone out there will know what it should be. I'm pretty sure that Protune gives a direct readout of the voltage but it's also easily done with a multimeter.
My basic thought is that the problem isn't the cooling system per se, but is another fault that is heat related but that won't be cured by changing the cooling arrangmeents particularly to a system that gives less cooling than standard when travelling at speed.
