"I have a lot of questions any help would be appreciated.

I build a homemade stianless steel valued reflex system.

If I boil water for first run will it clean it good enough? DoI need to add any cleaner/s?

I'm brewing 11 gallons with a mix of water, 18 pounds of water suger, Crosby & Baker distillers yeast, 8 tsp. of yeast nutrient and about 12 oz. of tomato juice. Started brewing in a 16 gallon stainless keg on friday. Hoping to brew next Monday. Seems to be bubbling and fermenting nicely.

When it stops bubbling and clears I plan on siphening off the top 10 gallons and let set overnight.

I'm planning to set both valves so half returns to the still and half is collected. I plan to collect in mason jars (what size do I need?) cover with coffee filters and let set overnight. Figure the first 2 and last two will not be blended. What do I do with them?

Plan on distilling from around 172 to 178F.

What do I do with the rest in the keg after I'm done distilling?"

Hey Bob welcome. On the storebought model I got they say to run some vinegar and water through it. Think I used about a gallon with 3 gallons of water. This be with your packing in there. Dittos to Bushy on the bunch of jars. I start collecting heads in little jelly jars after tossing a half cup of fores. I can now usually sorta guess when its going to start smelling right. As far as splitting the output you need to let it reflux for a while under most conditions..which is its recycling the vapors back down into the boiler but you aint taking no output. Hour is the rule of thumb. Then start collecting. That give you a real pure product..if thats what your looking for. I am running mine potstill/reflux mode today..pushing it hard and fast. More than one way to skin cats I guess. I am trying to wind up with some flavor:) Best of fortunes on the hobby.