Replace your TPS. When yu start the bike (unlike carb engines) you don't move the throttle AT ALL. The TPS sends a signal the throttle is off. What if you open the throttle when you start? The ECU assumes the TPS signal is in the "off" condition and adjusts accordingly. Let go an watch the engine do amazing things as it starves for fuel.
If your tune uploads only temporarily fix the problem the ECU is recalibrating based on sensor inputs as time goes by. You have to start somewhere to find the culprit so starting with the most likely candidate for your problem makes sense.
A note on coils. A coil going bad can also be intermittent. When cold the coil can work fine, but when you heat it up and the metal coils begin to expand a broken band can stop the coil from firing. You can check you spark leads in a dark (blacked out) garage by starting the engine and looking for sparks jumping to ground from the wires (it's quite a light show on old and cracked leads). You can't hear it but you can definately see it. If you have one bad coil you can find it by lifting the spark plug wires while the engine is running. There are three coils, two leads each to the spark plugs in a single cylinder. Pull the plug wires from the #1 cylinder and just rest them on the spark plugs and start the engine. At idle lift the wires and see if the idle changes (a.k.a the engine dies). It's that simple. When you do that and the engine isn't affected you have your bad coil. Some might think using a temperature probe on the exhaust header would also work (since the piston affected isn't firing). That works great for individual headers, but the Rocket's (including ALL after-market) pipes go to a collector so temps will be fairly uniform.
To make it easy you can just replace all three coils and wire sets and call it a day, but that gets to be pricey. I replaced both my coils on my Trophy with the Nology coils fitted to the Bonneville because they were the same part number. I haven't lookied into Rocket coils but I would guess the parts are similarly binned.