Bagel Question

Hi all- I am an amateur baker who does a small amount of baking at the restaurant I work at. I have been making bagels there for some time but have been having a lot of trouble with them coming out not as I would hope. Before making them at work, I had made them on occasion at home with no trouble. Usually would use Reinhart's recipe from BBA and just loved them. However, following the same recipe at work they come out unattractively yellow-ish (no browning whatsoever) and more concerning to me, very bumpy and deflated. They puff up well when boiling but after a minute or two of sitting on the pan, deflate. Still taste great but very unattractive. I have been experimenting with other recipes but still not loving them. I have two theories about what's going wrong, hoping you all have some sage wisdom and advice:

1) My boss (who does not love baking like I do) suggested I just use brown sugar or honey rather than malt powder in the recipe since it doesn't make much difference taste-wise. I always use malt powder when making them at home. Would that lead to the change in puffiness though, or just a textural change??

2) I just read in Baking Illustrated today that in order to achieve proper stiffness of dough, bagel dough should not be kneaded by hand and should never be doubled bc ingredients will not come together properly. I have been kneading by hand and usually double the recipe. Is this why? The doubling? Does anyone have a good recipe that yields a larger quantity of bagels, ideally 40-50?

Thanks so much!!