From experience as you will read I am one for a thorough cleaning of the carbs. Pay very close attention to the pilot jets. They control your idle circuit in the carbs and if blocked will cause a pipe to be cool to the touch at idle. Just take your time.

Give us some history on the bike.

the bike was bought as a easy project (put back together) it was sitting for about two years. put back together would not start starter button would not work no spark. so i bypassed all saftey switches still nothing. it turned out to be the sidestand relay(not the switch it self). took it for ride had no second gear. found a parchel bike with no title pretty cheap,that has been sitting for just as long . swapped motors. now currently have alt problem and this problem. i also had title problems. It still is not on the road, havent got the title back from the state yet. all in all the bike has been a pain in my butt ever sence i got it. i thought about just getting rid of it. but it is becomming to be personal challenge now.

I'm assuming you did a 600 to 600 swap. Doesn't matter. If you are having an alternator problem, it's a wiring issue or bad alt. With the bike running put a tester on the terminals to see what it's putting out. I don't really know what it is suppose to be. Maybe 13.5-14 volts?

The carb's are a major issue. Been sitting. A quick spray down the throat is not going to cut it. It's a total tear down without separating the carb's apart. You need to get every orifice open again. Most likely bad seals on all carb's also. These are common problems. Pilot jets are almost always the culprit at idle. Yes, my friend, you need a complete overhaul. Hard? Depends. The question is can you do this? Do you have wrenching ability. I don't know you. Since you did the motor swap, I say maybe. Just search and read and take your time on the carb's. I'm going to get flamed for this but Harbor Freight does sell seal kits that are made for gas use. I have used them. Go there if you are on a tight budget. Where are you located? What state?
OR, part it out and get something more complete.

me and newbie may have figured out the alt problem. i did take the carbs and clean them, well the top and the bowls did not take the jets out, but i am going to do that next. i am loctated about 20 min north of pittsburgh pa. there is a harbor freight out, here i will check it out. I have worked on carbs before but not 4 at a time or to far in depth. i have read carbs 101 doent seem to bad. i will have all winter to get it right. thanks for the help

As said already do one carb at a time and use carbs 101 as a guide and you'll be fine. Also do yourself a favor and replace all the JIS screws (looks like a phillips) on the bowls and the plastic covers with socket head cap screws.

i am gonna break them all down in separate containers and soak every thing for a couple of days in carb cleaner. i only want to do this one more time. i just ordered the seals and plugs. i am hoping that the jets are alright. not sure what the jis screws are, do you mean the drain screws or the srews that hold the bowl on.I dont remember seeing any plastic caps anywhere. thanks for the input

The jis screws hold the bowls and the black top covers above the diaphragms.

JIS stands for "Japanese Industrial Standard" It looks just like a standard philips. They can be hard to remove and a standard phillips screwdriver tends to tear them up. Replacing themwith a socket head screw just makes life eaiser down the road.

Well, I'm about 5 hours away so travel is out. There are other members in your area that can help. I did replace the bowl screws with cap screws from Lowes. Not a big deal, I think everyone else has gone that route also. Remember to pay very close attention to the cleaning of the pilot jets. Garbage bag ties with the paper stripped off work great for cleaning the air and fuel passages. I did pull my carb's of many times before and finally got sick of it and really scrubbed the pi$$ out of them. I didn't see a need to separate the carb's from each other so I didn't do it. Unless you are changing all the seals on the carb's. Less aggravation. It's good that you firgured the alt. out. Electrical can be frustrating. Lately I have been getting heavy into carb's and really getting to understand them. Keep us updated on the progress you make.

KatanaFreak93,

Its really not a good idea to use wire of any sort on the carbs. The passageways are aluminum and the pilots are brass, both are very soft metal. The wire will open things up Sure, but will also cause more fuel to pass than is needed. Especially on something like the pilot jet where the fuel amount is metered for a reason. Use fishing line to snake the passageways and pilots, you wont damage them with it.