If the engine is running properly for 20 minutes, and you have some valve clatter, I don't think think it's the valves. You've got compression and fuel. That's why it'll start and run for awhile. Something is changing as it gets warm that causes it to run rough. I'd concentrate on what can change as the motor gets warm: carbs, carb boots, your new ignition, fuel flow and coils.
First I'd get it warm and get it back firing and spitting. Then I'd try to figure out if it's running rich or lean: do you smell unburned fuel. If so, pull the air filters and see if it runs better. If you don't smell fuel, turn the choke on. Better with choke on? Pulling the air filter will lean out the mixture and turing on the choke will increase fuel into the engine.
Also check your diaphragms carefully. Pulling them out and carefully stretch the rubber looking for any pin holes or tears. If you find any or the rubber is hard, replace the diaphragm and recheck. I've had a bike run exactly like this: run fine cold and progressively not be able to take any throttle as it got worm and it turned out to be a hole in an old diaphragm.
Next I'd test for air leaks at the carbs: take WD-40 and spray it around the junctions at the front and rear of each carb and air box junction. If the idle changes, you've got an air leak. Fix it and recheck. Also spray around the diaphragm top and where the butterfly shaft is located on the carbs. These can leak too.
To test the ignition, simply remove the new one and put the old one back on. Some electronic ignitions don't work and you need to check the engine with a good one. If this fixes the problem, get a new electronic ignition. Your timing could be off, but it should run a little rough cold as well as hot with incorrect timing. Also I don't know if your new ignition has a mechanical advance or electronic. Again, mechanical one will not change going from cold to hot. An electronic one can fail as it gets hot if there's an intermittant short the opens with heat.
Test the fuel flow is easy. Ride for 20 minutes and get it running rough, crack the fuel fill and see if it runs better. All these bikes have some sort of fuel vent. You've got to replace the fuel in your tank with air or it won't flow fuel to the carbs.
As for the coils, replace them with the old ones and see if the problem is corrected. Also make sure your ignition leads are the correct ones for the bike. Some run resistence leads, some don't. I don't keep that in my brain. You need a manual to help get things set up correctly.
Do these things and let us know what you find. It sounds like a fun project.