some diagrams (yes they're awesome) for variations of rwd 20v water cooling configurations
http://www.toycrazy.net/tech/rwd20v.html
what you describe will work.
Just remember the back of the 20v overhangs the block by something like 18mm. so take that off the clearance you had with the 16v, then take off the thickness of the water blanking plate and bolt heads. Assuming this is for your ke20, it may be better for firewall clearance ( just under heater protrusion) to weld the holes shut and drill/grind a water passage at the rear of 20v head to connect back to the inlet side passage. This has been detailed in the club4ag.com forum in tech section - 20v. and could use the original radiator outlet port to feed your ke2 heater and connect it back in just before the water pump inlet. (theres just enough room above bellhousing and below head for a steel pipe connection back to inlet side.
rather than use the rwd bits (if you don't already have them). have you considered using a fwd ae92 remote thermostat mounted under the intake manifold? in conjunction with joining the water channels at the back of the 20v head and making water outlet at the front of head. can use 16v or 20v water pump (with the matching backing plate) for the thermostat to feed into. has room for fwd alternator and fwd alt mount too. cheaper and easier to source parts etc than the genuine rwd water system.
ps, if not using the original 20v water pump, the 20v timing belt cover has a mismatch. 20v water pump can be used with 16v backing plate if you either turn clearance into the plate for the impellor or trim the 20v impellor blades.