After installing my giant sight glass under my conical I'm a little conscerned that my racking arm wont reach far down enough to get every bit of beer off the yeast/trub cake at the bottom......especially after harvesting yeast. Has anyone had trouble racking off all their beer?
You're overthinking this, IMO.
Any time we move from a basic BK with a simple plastic fermenter to a system involving pumps and conicals and such, there are going to be losses.
On my CF10, I have the racking arm pointing all the way down. Now, I'm not doing hop bombs with all sorts of hop trub and cold break and other stuff in there, but IMO the sight glass actually serves to provide a reservoir to get the gunk down below the level of the beer.
Because I'm using pumps and a RIMS system, and with losses in the mash tun dead space, in the hoses, in the gunk remaining in the BK, with the conical and so on, I've bumped my recipes up 10 percent to account for that. It's just the cost for having a more flexible and capable system. That's how it is.
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I know that early on, you're not sure what you can and cannot do, so you're not sure where you can put the racking arm.
Try this: Set the system up w/ the sight glass and racking arm, then add a gallon of water to it. Lid off. See where the racking arm is in relation to the water, and you'll have a better idea as to whether you're above the yeast and trub. If you plan to harvest yeast, you'll draw off maybe a quart, so you can factor that in, too.
When I rack to kegs, what I do is attach racking tubing to a camlock fitting on the racking valve. It could also just be a tube with no connection on the out side. Then I'll run a little beer out that line to clear any trub that is in the racking arm (and there will be a little no matter what direction it points). When that clears--maybe a cup or so of beer at fast velocity--then I proceed to racking to the keg.
It'll depend what fittings you're using as to how you do this. My connection is made with this:
I often use this (available from brewhardware) in the OUT QD and it allows me to squirt beer out the end; it opens up the QD. That also lets me clear the tubing of air so when it goes into the fermenter, the line is purged.