Things to try
 

Try putting a piece of duct tape over the leaky shaft seals to see if that makes a significant difference. Also, if you haven't done so, check the float levels in the Webers. If the floats have leaked internally, then the fuel level won't be high enough for normally rich running. The carbs sound like they need a rebuild anyway. Does this engine use vacuum advance? if so, you can check function by applying a vacuum to the adv hose. Depending on mileage, check the oil cooler as it may need to be flushed out. Good luck!

A lean condition will cause a backfire in the exhaust, rich in the intake.

Answers to some questions raised.

Carbs were rebuilt with all new seals and new float valves.
Mixtures adjusted using Colortune and now run very well when warm
Fuel levels adjusted using the factory tool.
Oil cooler was professionally sonic cleaned.
Fan is 11 blades.
Pulleys are all stock.
Air guide on the back of the alternator is on there.
There is no obstruction under the shroud as it was just assembled at the time of the valve job.

Duct tape at the throttle shaft is a possible idea.
I am going to replace the two pressure relief pistons and springs.
We will also remove the oil tank and flush boil it out as well as replace the two short hoses to and from the tank, They are old and leaky anyway.

After that, I am out of ideas and the engine would come out again to be stripped down to see if anything else is wrong.

OK...my brain still running in overdrive...LOL
Is it possible that there is hot air coming from under the engine in any quantity (holes in engine tin...or poor seal around the edge)..?
Or...you have no heat exchangers...and the piping is not connected...or...the engine lid is blocked or a custom grill has been installed letting in less air than the stock one?
Bob

Let me summarize this thread because the information is all spread out ...

1. Car was running hot before valve job and it was suspected that the oil cooler was partially blocked.
2. Proceeded to tear down and did a valve job. No mouse nets found, no obstruction found, just a lot of leaks. Did not remove pistons/cylinders and did not split magnesium 2L case.
Heads sent out, got back, and assembled with new cap, rotors, plugs, ignition wires, all new gaskets and seals, new chains, four rocker arms replaced with those from 3.2L engine, cam towers cleaned, two long oil hoses replaced, oil radiator sent out for ultrasonic cleaning.
3. Other work includes rebuilding of carburetors where 0.45 idle jets were replaced with 0.55 jets (did not fix one leaky shaft), rebuilding alternator, already has 11 blade fan, cleaning of shroud and air funnel and tin pieces. Stock heat exchangers are on the car as well as heater valves connected. Some of the air rubber seals around the engine bay is broken off but the sealing is still good. There are no holes in engine tins. Heater paper hoses are replaced with new. Car is very stock for a 914-6

After assembly of engine and tuning of carbs with Colortune, car runs fine at 3000 rpm but runs hot above 4000 rpms. Things that have been checked are:

Function of on engine thermostat with water bath, works fine.
Distributor advances to 30 degrees BTDC at 6000 RPM
Oil pressure at 60 psi with mechanical gauge at 6000 RPM, idles at 10 psi
When engine off, reach in to feel belt tension. Seems OK.

Clues:
Carbs spit when cold but run very smooth when hot.
Some popping in the muffler when cold, but none when hot.

To try next: replacement of two short oil lines at the tank, flushing the tank, replacement of two pressure relief and bypass valve pistons and springs.

Cylinder Air Deflectors
 

As mentioned by HawgRyder it seems that possibly the cooling tins (cylinder air deflectors) around the cylinders may be the culprit.

Did you remove them during the top end build? If not then they may have been on there wrong before causing the overheating issue all along. They can go on back-wards, but wont work, symptoms are of improperly installed fins are as you describe.


http://forums.pelicanparts.com/911-engine-rebuilding-forum/238294-cylinder-cooling-tin-arrangement-puzzlement.html

I've seen pictures posted by members of this forum showing off their work with upside down tins...definitely worth a double check.

Weber
 

Check the emulsion tubes and air correction jets to make sure they are the correct ones for this application. Since the engine was running hot before as well as after the valve job, the problem is in something that you didn't touch. Improper air correction jets can allow the mixture to lean out at higher rpms. Probably should find the specs for this engine and go from there. I was able to find this for the 2.2 ROW engines. This should give you a starting point.

Venturi 27mm
Preatomiser 4.5
Main Jet 110
Air Correctors 185
Emulsions F1
Idle Jet 45

So we got time to pull and replace both oil pressure bypass valves yesterday. We are also changing the oil line and cleaning the oil tank. The carb jets were removed and inspected and ...

Main jets are 105
Air correctors are 170
Idle jets are 55 (previously 45)

So, I am going to up the main jets to 130 to see if it runs less hot.

Main jet sizes.......
 

105 to 130 main jets is a pretty big jump. If it were my choice, I would try 110 or 115 mains first. Also, what are the emulsion tubes? They probably should be F1s.