What temp. are you planning on baking them? If this is long term process I would recommend that you hav trays made out of an appropriate ESDS material that can withstand your bake temp (such as duropol)for your QFPs. You can have several patterns/packages all in the same tray. The use of a GOOD vacuum pen from my experience shows that damage is almost non-existent when transferring QFPs from here to there (obviously operator dependant) If you are really worried about bending leads during a transfer you may want to write a machine program to pick from stick and place into tray or tray to tray etc... I have found that returning components to sticks is where the damage/polarity issue is most likely to occur.
The BGAs I wouldn't worry about to much since they are pretty durable. I would set them on a plate ball up and go as you suggested.
Russ
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