so ok....on my 64cc airsal kitted a35, I run a 15:15sha with that same intake and airbox. I use the metal mesh element that comes with the SHA and the airbox with the plugs removed and the bike runs great.
As far as those boyesen reeds go, I always thought they were kind of gimmicky. I really like the stock Airsal Reeds, the rubberized Athena Reeds or the Doppler ER2 reeds. I'm running the ER2's right now and it added some performance i think? It felt peppier, but I also upjetted for colder temps/the new reeds at the same time so like who really knows?
anyways, I wouldn't go drilling anymore holes for flow or gas drainage, but you should move it away from the side cover, unless you have that portion of the side cover cut away. If that portion of the side cover is cut away, I think the position of the airbox is actually pretty optimal (and exactly the same position that i run mine in.)
also, I would make sure everything is good with the rolling frame before doing any cylinder porting. We've got some spare a35 cylinders, pistons and stock heads here that I would sell if you wanted to give porting a shot without having to port your good cylinder.