What would you do?

Absolutely NO WAY would I put manifolds on a ANY performance oriented build unless it was due to a race class restriction. For example: Take a deep breath through your mouth, insert a coffee stir straw into your mouth, and now try to exhale....a bit of an exaggeration, but this is similar to what you are doing to a stroker engine with tiny exhaust manifolds. The better the engine can breath (move air/fuel), the more power you can make.

Get some good headers (not cheap-o's) and you will have plenty of ground clearance. Can you see my headers hanging down.....nope, they are just a tick higher than my low profile pan. I had some cheap-o black jack headers YEARS ago...flattened them when I hit a decent size dip in the road...never again.