For anything carb related, call Pierce Manifold. They have a Weber manifold that will fit the B6, and can help you with any linkage, jetting, and accessories you might need.

 

Machining some stock manifold runners to fit Bike carb hose adapters could be one way, low cost and a lot of work. I think the Yamaha R6 is 38mm which would be on the big side of things.
R6 Carbs: Motorcycle Parts | eBay

DCOE is only an advantage if you get the angle right, Webers etc needs to be within 7 degrees from level IIRC.
And those Webers are not cheap anymore. Mikunis however...

 

The fwd dohc 1.6 came in the 91-94 mercury Capri. It was also in certain years mx-3 but they had a different head than all the other dohc 1.6. The exhaust manifold will bolt up but the intake is different. Also you may have some issues with a carb intake manifold designed for a miata hitting the firewall. When you go turbo the miata 1.6 intake manifold will be really close to the strut tower and be pretty much impossible to get a intake pipe on.