Phil,
Very little fundamental difference in modifying a Vans cowl or a James cowl. The stock cowl is a honeycomb and thus may need core hard points here and there. I suppose you could argue it makes the stock cowl harder to modify, but I don't think it is a big deal.
Going with a horizontal manifold means using a snorkel from the left cooling intake, or using a forward facing scoop through the cowl. I assume you're thinking about an RV10, so you may want to contact Rod Bower regarding one of his scoops for the -10 cowl:
http://www.vansairforce.com/communit...32&postcount=1
The obvious alternative is to build whatever you want:
http://www.vansairforce.com/communit...ad.php?t=41375
Remember, this is all about education and recreation......learn new skills and enjoy the process.