I'm running a Mercury 525efi with Hurricane lite headers in a Fountain sportfish with stepped hull. Headers keep getting too hot when I run hard. They just aren't getting enough water with my current setup. I'm running a dual pickup Bravo XR lower. When I get the boat trimmed up where it likes to run, I get too many bubbles and the water pressure jumps up and down on the gauge in unison with hitting waves. This is what I'm thinking about doing:
Close off the side inlets on the drive.
Add a transom mounted water pickup.
Plumb the water from the current drive hose and the transom pickup water into a sea strainer with two inlets and one outlet.
Install a two stage water pump that pulls from the sea strainer.
Has anyone tried this setup? I've replaced my water pump and checked every inch of my cooling system for corrosion, blockages or kinks in hoses. Everything is completely clean and clear.

Have you eliminated the hose that runs between the back of the header water supply to the tailpipe? This thread might help:

525 CMI , Hose from header to tail pipe ?

Yep I removed it when I went from the stock CMI headers to the Hurricanes last year. I've also tried it with restrictors in and removed. I was scratching my head until I hooked up a clear hose to the port side header. As soon as I trim up a little bit it turns white almost like there's foam in the lines. My theory is that the side inlets on the drive are not getting good suction and are sucking air in.

Duplicate post

Try plugging the top 2 holes on the side inlets with 1/6 brass pipe plugs. Or else you plan sounds good but possibly not needed.

Have you checked drive for corrosion where hose connects?

I forgot completely about that!!

I haven't pulled the lower but when I back flush there's no restriction at all. It's worth a look though. Would that create bubbles in the system? It seems to cool ok at slower speeds.

How far up are you trimming ? where is the prop shaft in relation to the bottom of the hull

not at the lower. It’s where tube is plumbed from sea strainer to outdrive in bilge. On the transom assembly