Loic,
There are enough reserve pilots, many with many hours of flying experience and combat experience still in German awaiting new planes. The 1000 wont make that much difference. Also the pilots coming out of the old German training program still are getting over twice the training time that the Allied pilots are getting at this time.The German's are also training 3 times the pilots that the RAF is at the time. Also as of the BoF, there was roughly just under 500 RLM active pilots with some form of direct combat experience. Out of over 9000 pilots, that's not enough to differentiate between green and experienced pilots. As for the placement of the Luft's afterwards, I've already commented that the two Luft's historically in France might have to have their borders changed and even have a third one put in the south of France. BTW this will mean that ships coming through the Straits could be directly attacked in the Med. if that happened. Don't forget that we also have the option of the RLM drawing from the 2 unengaged Luft's for pilots, crews and aircraft.
Also they are facing as of June 5th just 475 RAF fighters of which only 384 were servicable front line fighters ( 179 Hurricanes and 205 Spitfires ). Also neither of these aircraft at the time had armour and few had self sealing tanks.