On the Rocket (see avatar) I riveted galvanized sheet metal to cover the spaces where I had removed the windows and tracks. Had I used aluminum on my steel-bodied bus, I would have had major problems with electrolosis (is that the right term or is that for hair removal?) between the metals causing corrosion. I did have aluminum emblems on the side of the bus but I insolated them from the steel with a rubber gasket, cut from an old inner tube and plastic nuts, washers, and bolts.
The drip rails could probably be removed without major leakage, provided you employ a vigorous amount of caulk, but with the way a bus body flexes and twists, it would be a constant issue. I know you are going for a smooth look but those drip rails do a great job of shedding rain water. It's a real drag to wake up in a thunder storm and see water leaking onto the wood floor of the cabin from the inside of your insulated walls! As you can tell, I'd leave the drip rails alone but I also know that practicality sometimes takes a back seat to art. Just make sure you have a mop! Of course, if your bus body is already aluminum, you could heliarc the panels in place (with drip rails removed) and simply grind your welds smooth.
The rub rails do more than strengthen the sides of your bus. They also support and stiffen the thin sheet metal skin of the bus and keep it from warping. Those panels can actually rattle at speed. When I covered my old window openings I had this problem and had to salvage more trim (rub rails) from another old bus and install them. Go to http://www.gentlekharma.com
and click on the Rocket link to see what I mean. It worked great.