There's a myriad of ways to clean mill finish aluminum. Pick one and for the most part, a water-based primer and paint should work, if you don't have access to a spray booth. Aluminum expands and contracts at a very face pace and so does your latex paints, so it should bond well.
As for a seam, why would you use vinyl too small to do the job correctly ?? Get the size you need and do it right. Honestly, that's one of my biggest pet peeves........ using wrong materials when you know better. Sure it's gonna cost you more, but isn't your customer worth it ?? You're skimping out on a free piece of expensive substrate and now you wanna skimp out on your other supplies. Do you wanna do this job with basically nothing outta pocket and charge normal price for a half-a$$ed job ??
C'mon, either do it right or pass on it.