I own 2 650c recumbents. I've found no disadvantage to 650s vs. 700s and I have over 100,000 miles on 700s.
I currently run Velocity Spartacus Pro wheels and Mavic Ksyrium Elites. Velocity also makes Uriels which are nice. If you have the cash, there are high-end wheels available like Hed 3s, Zipps, Rolfs, etc.
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Keep the chain tight!