I have a 1994 tw200 that has been stored in a garage for about 5 years. I have drained and cleaned, but the bike will not run with the choke disengaged unless I give it a lot of gas. It will die when in idle. I have been told it could be a pilot jet, but do not know what to do.
First off, you know the bike runs, but it is nowhere near ready to be ridden. Do a complete service, front to back, top to bottom. Clean, lube and adjust everything to spec--cables, chain, valves, swing arm, oil and filter, air filter, ..., everything on the list--it is way over due for a complete service after being parked for 5 years. You'll probably need a new battery. Make sure the inside of the fuel tank is clean and start with fresh fuel. Other than that, I wouldn't spend any money other than a can of carb cleaner until the bike is running properly.
Your bike has the typical clogged pilot circuit common on bikes that have been improperly stored. Since the bike won't idle at all, more than likely the pilot circuit is completely stopped up. The cure is to completely disassemble and clean the carb. Once all the rubber and plastic parts are separated from the metal parts, clean the plastic and rubber parts with plain old dish soap and water. Road dirt on the carb body can also be removed with dish soap and water. Blow dry with compressed air. Run a soft copper wire or plastic bristle through all passageways in the metal parts, give each passage a brief squirt of carb cleaner. Let soak a few minutes, run the wire or bristle through again, squirt with carb cleaner again, repeat as often as necessary. The hole in the pilot jet is very, very small. You may need to strip a piece of light speaker wire to find a conductor small enough to fit. An old toothbrush helps carb cleaner get the yellow-brown shellac out of the bowl. Once all passageways and holes are clear, blow out with compressed air. Reassemble carb. Set pilot screw at 2.5 turns out for an initial setting.
Once you get the bike running, all the other service is done so you can ride with peace of mind while deciding if you need to rejet or not.