Rely on your experience. The software is only a tool. Plug your known boil-off rate into Beersmith. This should reduce your process water by 1 - 1.5 gallons.
To answer the question in your first post, yes, there will be enough yeast in suspension to bottle carbonate your beer; you will not need to add new yeast.
As for Biofine clear, I've found it to be worse than useless. YMMV. If you don't have a vegan issue, nothing beats the combination of...
If you're a fan of Ballast Point Grapefruit Sculpin, Northern Brewer has a clone kit called Grapefruit Pulpin'.
http://www.northernbrewer.com/grapefruit-pulpin-all-grain-kit
It features Chinook, Cascade and Amarillo hops and dried grapefruit peel that you soak in vodka for 2 days before adding...
I started all grain brewing by mashing in a bag in a 5-gallon cooler because I got the cooler for $12 at Menards and a mesh bag from Northern Brewer for $5 instead of buying the Fermentors Favorite Essential All Grain Brewing Starter Kit for $199. According to The Green Bay Rackers...
For what it's worth, this is the method I follow:
http://brulosophy.com/methods/lager-method/
I use the alternate method without gradual temperature ramps. So far it's worked exceedingly well for me.
I'm not sure how that would happen. The assumption is that you are cold crashing after fermentation is complete, the yeast have consumed all of the sugars that they will consume and have gone dormant, while ester production is something I would associate with active fermentation. That said...
I'll also sing the praises of Wyeast 1272, although I've never had any trouble with flocculation. And I dry hop first and then cold crash with gelatin.
Think of a 5-gallon batch that sits in a carboy for two to four weeks at room temperature as a giant starter. So no big deal with your starter sitting out for a couple of days...