Did the engine hesitate and miss like this before you had it rebuilt? If not, then something wasn't put back together/on correctly, when the engine was reassembled/reinstalled, more than likely.
New spark plug wires can be bad out of the box. Do you have the old wires around? Did it run fine with them on it? If so, then swap one of the old wires for one of the new wires and see if it runs better...do this for all 4 wires, until you have all 4 old wires back on the engine.
Are you sure you have the plug wires on the correct cylinders? If you have 2 on the wrong cylinders, then it will run poorly (probably wouldn't even be driveable).
Another thing you could try, is to pull one plug wire off while the engine is running. The engine should run noticeably worse, when a plug wire is pulled off the spark plug. If it doesn't, then that plug wire, spark plug, ignition cap tower, or cylinder is where the issue is. If it runs worse, put that plug wire back on and pull another one....do this for all 4 and check the results.
I didn't see where you replaced the ignition cap and rotor. I'd recommend doing that too, if they haven't been replaced recently.
How high is the idle? A vacuum leak, or a line in the wrong place can cause high idle. A high idle after initial startup is normal, until the engine reaches operating temp. But after warmup, it should be right around 800rpms, with no electrical load (lights off, AC off, etc.).
Are the valves adjusted and adjusted correctly?
To check to see if the EGR valve diaphragm is stuck, you can push in on it, when the engine is off. It will probably push pretty hard, but if it moves, then it isn't stuck. I use both hands, 2 fingers, 180* apart, to push on it...ensures I am pushing evenly and makes it easier to push than just using one hand.
Are you sure your crank to cam and cam to distributor timing is correct? It is sometimes hard for people not familiar with these suzuki engines to get it set correctly. If the crank mark is at 12:00 and the cam mark is at 12:00, then the distributor rotor should be pointing to the cap tower that the spark plug wire that runs to spark plug #4 is connected to.