I'm pretty sure your crush is way too coarse. Let them run it through twice or better yet adjust the mill. Look for pix what a good crush should look like, a little flour, no whole kernels, and no bits larger than around 1/16". Depending on your mash tun and methods you could go as fine as you dare.
Brewing in 2 kettles is fine. As a matter of fact, you could boil down your 3rd runnings (2nd sparge) longer to condense it more and add it later, keeping the total gravity up. Then again, energy may cost more than an extra pound of base malt.