Not being able to try before you buy in this mail order world of ours is a right royal PITA!
New bike feels much roomier with the longer stem and I can't say it's had any real effect on the handling that I've noticed, as I only rode it a few times with the shorter one on it. When I bought my first MTB I was a roadie and wanted a racy stretched out position, so maybe it is that bike that is too long, as opposed to the new one being too short? Times and trends change, don't they?!