Pete and all this is a really great discussion.
My main function in this realm is malting, and I spend a lot of time and money kilning grains. I think there are a couple of points here that i would like to make:
1. Kilning is done to stop germination and preserve the grain in it's "modified" state so that it can be used months or even years later by brewers & distillers. Getting the correct moisture really makes a difference for getting the correct grind when you are using a roller mill, however if you are using a hammer mill you are pulverizing everything and most likely have a way of filtering out the fine particles (mash filter vs. lauter tun in the brewing world). Also kilning helps to remove some of the tannins in the grain, and thereby enhances the flavor. In generic terms, the higher temp the kiln the more flavor develops, however this higher temp kills off enzymes needed for mashing. There are literally text books written on kilning and malting, so I will stop my explanation here.
2. The rootlets are a pain to take off without damaging the grain when malt is green, however when it is dry they literally fall off when you rub the dryed malt together.
3. Rootlets are both high in protein and high in tanins, plus they look bad, so that is why they are removed. The added protein slows a mash and the tannins add off flavors.
That being said, I think you should try using green malt in your distillates. If you are malting in your distillery so that as soon as you have full acrospire length you are mashing in, I don't see a problem. You will have very good DP. My only concern would be flavor - if you could use green malt to brew with, believe me Anheuser Busch would be doing it, but they use dry malts because green malt adds to bad flavor in beers. If you are distilling, I don't know this for a fact, but I would hope that most of those off flavors are removed during the distilling process. If you try it in a batch and it comes out good go with it, kilning is by far the most energy intensive portion of malting, and you will save all that effort by using green malt. If it doesn't come out that good, you may be able to dry with a smoker - we do a few smoked grains that I dry with a wood fire, you may not have to dry them down as far as you would if you were ordering this malt or storing it for long periods but again would depend on rootlet removal, and grinding method.
As far as consistency goes, I wouldn't be concerned, if you are malting on such a small scale, consistency is going to be a problem whether you are kilning or not. The only reason the big guys are "consistent" is because they have such volume they can blend batches in order to have a "consistent" product. Malt is malt, and you may not get 80% extract, but if you get 60% is that going to be a problem? By using a low or no kilning temp, and assuming your grain is a good malting quality, the diastatic power should be pretty good, even though extract is low.
Sounds like a great project you are working on.
Cheers,
Christian