Hi Steve,
Have no fear! Fabulous bagels can be made at home.
We can probably help more if you tell us about the formula you are
using. I use the one from Peter Reinhart's Bread Baker's Apprentice
and always have great luck with it. That recipe directs you to form
the bagels, cover them, and refrigerate them overnight before boiling
them. With bagels (as with most bread) time = flavor. This
refrigeration technique gives the bagels plenty of time.
I've never tried substituting molasses for malt powder. Might work...
(Diastatic) Malt powder contains enzymes that convert some of the
starch into sugars...molasses just adds sugar.
But I'd try to get diastatic malt powder first. Try a local beer
brewing supply store, or order it online from King Arthur.
Best of luck,
Allen
SHB
San Francisco