Get some wash-off spray-on chalk (essentially spraypaint that won't survive the next rain, because it's made to disappear when hit with rain/a hose). That should give you sufficiently uniform surface emmissivity to deal with those problem spots.

Thanks!

Do I do the measurements from the outside then, not the inside? Seems difficult in some cases unless I have a drone (roof, other hard to reach areas).

Do you know if i can find a tutorial anywhere? I tried googling, but couldn't find anything easy to understand.