I noticed that occasionally my RT3 would take a long time to restart. It appeared random, but as time went on, I realized it happens when engine is up to full temp on a hot day and I stop for gas, then restart. Thinking it may be a heat soak issue where the airflow keeps temps in check, but after sitting for a couple minutes, then trying to restart the impacted component won't work until it cools down. The coil is above the cylinder head and thinking it may be that, but also read about potentially the magneto or even fuel percolation. I didn't see any hits on this forum for my issue, but saw other bikes reported this issue. Wondering if anyone had experience with this and what the solution was. TIA!

Not hard to pull the plug and check for spark...  or use a spare plug.  Remember that spark can be hard to see in daylight.

Most likely a "fuel" issue...  what we used to call "vapor lock".  Ethanol blend fuels are more susceptible to this...  though we see it less in cars today because most don't have carbs anymore.  Do you have the phenolic spacer and two gaskets between the carb and manifold?  That part helps keep the engine heat from getting to the carb.
 

Yours might have one gasket and an o-ring.

I tried to remove the plug and check for spark, but my limited toolkit couldn't remove the plug when hot. Need to get better tools to fit in the tube. I use E0, but under rare conditions I have to use ethanol fuel, I put in the bare minimum to get me to a station which has E0. The last time this happened there should have been very low percentage of ethanol fuel if any. Below is pic, there's a black spacer and this carb has an O ring which I replaced when I cleaned the carb.

Random issues like that are difficult to pin down. On restart does it give a flooded up start like needs full throttle & kick. Or does it need choke to restart. Or has it got a mind of its own & just thinks --I'm rested--lets go.

When it starts, it's fine, no cloud of smoke or anything unusual. Runs like it never had a problem. At least it's predictable, lol.

Hi. I too have had problems along the same line on my RT1B. Now I know the cylinder induction method is different, but the carbs are similar I  the way they mount.
 ext time you remove the carb, remove the O ring from the flange side and put rhat flange on a flat surface to see if it's distorted. If it is, get some 400s rough paper, a flat surface and start rubbing it down until it's flat. Reassemble and you'll probably find that that was your problem. Mine was busting my balls, ( doing my nut in if you're English) but it's right as rain now.
Of course it may not be that ! 
regards
Dave.

Also if you replace the Oring in the flange, don't find a fatter one thinking it's a better idea because you'll end up pulling the flange ears around due to fat Oring having nowhere to squeeze into in the groove.
Also--another also--if you have to take heaps off the flange as i have with a coarse file rather than try to bent the ears back [that's a no no] you may need a slightly smaller section Oring. All my comments are to extreme cases--but have seen them all in 50+ years. Those early carbs are made out of Cheese or something?.

Thanks all, I replaced the o ring for another issue a bit ago. Original was larger than the oem one I bought. Temps are lower now, will need to wait until hot temps return to troubleshoot.

Took bike for a shakedown loop to reproduce the issue. Instead of stopping for gas, went home, shut off bike, opened gas cap and waited for 2 minutes. Closed gas cap and tried to start, but nothing. Attached plug wire to plug and verified no spark, so coil, or magneto, or something else heat soaks when stopped and needs to cool down until it works again. At least I have a direction.