I'm in the middle of such a swap. I have a Windsor block stroked to 424 CI with earlier A3 heads (I also have a set of C302Bs but the A3s are on there for now). The cooling circuit mod to the heads is no big deal. You just plug one hole in the head at the deck surface and do a small gasket mod. It's easily changed back. There's a web page out there that describes this in some detail for Cleveland style heads. If your interested, e-mail me and I'll see if I can dig it up. Somebody else out there will have to confirm the Yates configuration. They may be different.
Anyway, the motor mounts, flywheel/clutch, and ZF mounting are all the same. The cooling circuit may take some effort if you want to use a Windsor style water neck integral to the intake manifold. This was my choice. I'm fabricating a new thermostat housing and stainless tube that takes an immediate turn at the water neck and runs to the pressure tank similar to the stock set up. This deals with the bulkhead problem you mention. If you don't use a Windsor style intake, some guys put fittings in the front of the heads at the water jacket and remotely locate a thermostat housing.
If you're talking a Windsor style block, you probably will have a 9.5" deck instead of 9.2" like the Clevelands had. Intakes for 9.5� decks and the Cleveland style high port heads on the a 9.5� Windsor deck are scarce. I found a rare C351 intake that has Windsor style valley rails, 9.5� deck, and for the high port location (not cheap I might add, but very nice). I'm not that familiar with the newer Yates heads and their intake bolt pattern. I know they take Jesel style rockers instead of Cleveland type canted valve train and girdles. Better check with Ford Motorsports on the intake. Seems like I've seen a Y351 air gap intake that might be the ticket. If the Yates heads are the same as A3s or C302 port and bolt position, I have an intake and nice set of adapters. The extra deck height may also reduce the clearance between your exhaust, half shafts, and rear control arms. Headers for the Yates port position and bolt pattern are also likely a custom job. This is the case on A3s and C302s anyway. Besides this, you'll also have to fab some new air conditioner and alternator bracketry and/or perhaps some doinking around with pulley alignment.
More work than I anticipated. In my opinion it's worth it if your doing it for a Windsor style SVO block or maybe even a Stroked 2-bolt Windsor with a main girdle. They also have a little thicker cylinder walls than Clevelands, robust webbing, and very large 2-bolt caps. The Mustang guys sure seem to have a lot of fun and success with stroked 351Ws. My project is on Mike Dailey's sight (Panteraplace.com) in the Panteras under construction section. I'll be adding to it in the not-to-distant future. Check it out and if you want more info or the intake, e-mail me.
With the effort it takes to do it right, you need to ask yourself; why? I think the answer is for big displacement stroker and economy. There's more clearance between the pan rails on a Windsor so you don't have to grind clearance in the block even at 427 CI. The higher deck also gives a little better rod ratio. 351W blocks are inexpensive and plentiful. -Good luck.
