Yes it would be a good idea to clone your mother if you don,t wana lose it.
I would take as many clones as you can get off it , as you will have less sucsess cloning a plant this far into flowering and also your mother might not regenerate.
Yes it is normal for the lower branches to be small so take as many of them as possable.
Rooting will take up to a month so be patient with em.