1. I'm not sure that the pilsner has enough diastatic power to convert all of that flaked grain.
I'm not sure about this either, but I can say that I based this recipe pretty closely to Jamil's Witbier recipe he put in BYO. I've been taking his word as gospel recently for recipes and I've been succeeding, so I trusted this recipe fully. But I will definitely look into that.
2. Did you do anything to adjust your mash pH for mash this light? Mash pH can have a big effect on conversion also.
Water chemistry and mash pH are quickly rising to the top of my list of brewing techniques to work on. What would you should suggest for adjustments on a beer like a Witbier? Or if you have any sources you would recommend? Currently all I do in these respects is use a carbon filter for my water and use a pH strip to check my mash pH (when I remember), then I look at it and say, "Oh, cool." and move on.
Thanks for the response!