+1 for not using T-cut its horrible stuff.
regarding your roof, it could be tar spots but unlikely due to there location on the car and only seem to be in a localised area, its possibly tree sap that have gone black through traffic film contamination ie exhaust fumes,break dust etc.
as chris said try a clay bar on it which should remove it easier and will not damage your paint,also try tar and glue remover, to minimise this happening again clay the whole car, polish, seal it twice then two layers of good quality wax, this will stop contaminents bonding to the surface, also get a good wash routine going if you dont already, once a week if possible but twice a month is cool.
