Your original sequence is good, except for one step you have out of place--sanding.
You need to glue everything together after you dry fit everything. The glue will ooze out of the joints someplace- it happens. If you can force a joint flush on dry assembly, I will guarantee you that it will not be the case when you glue it up. Sanding after glue up will rid your project of the badly stained areas where the glue oozed and was only wiped up, preferably with a dampened cloth. Used the dampened cloth anyway during glue up, it make the finish sanding so much easier.
Sanding after glue up will give the chance to flush up slightly misaligned surfaces during the glue up. I go over all the joints carefully with a random orbit sander then hand sand it all in the direction of the grain. Most of the time the joints have such a small difference it can all be done by hand.
If you do have floating panels in you work, DO pre-stain the panels at least one coat before assembly.