Truck is running rough. Changed intake gasket, brake booster, and put in new spark plugs. Truck runs good for a few miles then it runs rough again. What could this be?

try this simple test
put in drive k with the hand brake on only ( no foot brake )
if it idles good then no problem now put your foot on the brake
if it dies out or runs rough , replace the brake booster as it is allowing air into the manifold and upsetting the air / fuel ratio

try running the fault codes to stop wasting time and money for starters , then fix what is needed only

Looks like you covered just about everything outside the engine.
Since it has 225k on the engine, its possible the valves are carboned up or burned to where one of the intake valves fail to close some times.
You might try a compression test or use a vac gauge when it is running rough. If the problem was not happening before you changed the plugs, you could have bought some defective ones.

The upper intake plenum is leaking coolant into the cylinder heads. The head gaskets on this motor are awesome. So, chances are it's the upper intake plenum. You can check this, by removing the vacuum hose that runs between the upper plenum and the brake booster. Stick your finger in and try to touch the top of the lower intake manifold. If your finger is wet it the upper plenum. You might as well replace the lower intake gasket while you're performing this work because they are prone to failure also. Use a shop vac to pull any coolant out of the cylinder heads. Get brand new spark plugs because the old ones are probably fouled. Once you get the plenum and gaskets replaced, remove your fuel pump relay and leave the spark plugs out and turn the engine over repeatedly for about 10 seconds to push any excess coolant out of the cylinder heads. Then, put the spark plugs in and turn the engine over for 10 seconds again. This will burn excess fuel as coolant out. Then, replace the fuel pump relay to allow fuel to be pumped into the heads. Car will smoke for a few when it fires up, but will clear out quickly. CHANGE THE OIL! Twice within a week if possible.

run the fault codes to find which sensor is failing from internal heat build up
when allowed to cool it works fine until it gets hot again

I would check the fuel filter, it should be changed every 20,000 miles or so. Also I would check the fuel pressure at the test port. I would also check for a weak ignition coil.

ROUGH IDLING CAN BE CAUSE BY MANY THINGS.I AM LOOKING AT LEAKING VACUUM HOSES OR INTAKE MANIFOLD GASKET LEAK.DIRTY FUEL INJECTORS AND WORN ENGINE VALVES WILL CAUSE ROUGH IDLING.ALSO LOW IDLE SPEED CAUSE ENGINE TO RUN ROUGH.

24 mpg on the highway is actually pretty good for that truck. at 48000 miles and being 3 years old its time for plugs, air filter, and fuel filter if available. thats cheap maintenance for now. but if very self conscious, run some fuel injector cleaner first, then change the plugs, because any octane booster or fuel injector cleaner can run the risk of fouling out a plug, by creating a hotter spark then what, normal gas does. the burn is hotter.

need to pull plugs and crank over in morning and see if water blows out of any plug holes. Sounds like water in cyclender.

My problem was solved when I repaired my 4 wd activation dash switch. The switch was contacting on 2WD & 4HI at the same time. The front differential activation is vacuum activated possibly creating a tug of war that didn't actually engage it but drained off vacuum from the engine? A theory at best but stumbbled across it because I knew the switch wasn't working properly I repaired it and low and behold rough idle disappeared and all is good for 3 weeks running.