You'll need a check valve in series with each pump, since the pressure differences created any one pump driving from the manifold will induce a reverse flow on the others. On very high head loops that may never present a practical issue, but on shorter hydronic loops that back flow can create unintentional heating of the "off" zones.
When reconfiguring, try to avoid micro-zones, since that causes short-cycling efficiency losses and unnecessary wear & tear on the boiler. If your current smaller zone 2 has just a low-mass stick of fin-tube for a heat emitter, it's almost certainly short-cycling on that zone. Zoning it by floors is usually pretty reasonable, as long as the room-to-room balance has been properly dealt with by load-proportional room-to-room radiation sizing (based on the room-by-room heat loads, not the square footage of the space.)