Put everything back together. When you go to start it, it will generally take some cranking and run rough for a few minutes. Black smoke will come out, this is all the crap coming out. Let it idle for 1 minute, after it idles well, then twist it up to about 3000 RPM. Hold it there for another 2 minutes, this helps it get hot and warm the bike up. After its warmed, give some good revs, more black stuff will probably come out. Then go for a ''happy'' ride and blow the rest out.
When running a high dose of SeaFoam in the tank, and doing the chamber cleaning, expect the exhaust to smell a little weird. I use SeaFoam in my bike about every 3-4 tanks. Generally 1/3 of a bottle. At the beginning of the season I do everything I described above.
The easiest way to clean a chain is with a rear wheel stand, otherwise when its time to move to the next section of chain, you'll need to roll to bike forward.
Pour some torch oil into it's own bottle lid, then dip the toothbrush into it. Pick an easy to reach section of chain (remove chain guard if needed), and lightly rub the oil into the chain. Choose about a 6-8 inch section to concentrate on. Rub the oil into all 4 sides of the chain, both sides, top and bottom. Rub lightly at first to allow to oil to get into things. After a few light rubs on all sides, scrub harder where needed. Keep in mind that you should be dipping your brush in fresh oil often. Scrub all 4 sides until all the gunk and dirt is gone. Then either roll the chain forward (rear stand), or roll the bike forward (no stand) enough to get the next section of chain into the 'cleaning area'. Repeat the above cleaning process. Keep repeating the whole thing until your chain is all clean.
Now your chain is clean, but there will be leftover Tiki Torch Oil on it. Grab a terry cloth towel, or something similarly absorbent and start wiping the extra oil off. If you were rolling the bike forward to scrub, you can now roll it backwards to dry the sections of chain. Keep an eye on the rear sprocket, as lots of excess will be there. Keep wiping that area down, might as well clean in up too.
Now that the chain is clean and dry, you'll want to go for a quick ride to warm the chain up and sling out any oil thats left in there. About a mile or 2 should be fine. Come back and do a quick wipe down again.
I recommend using a good aerosol chain lube. That way the pressure helps push out leftover cleaning oil, and push the lube into the small cracks and crevices. I use Honda HP Lube. It's not that sticky crap that gets everywhere and is a pain to clean up. It works great and keeps things quiet. Also, it doesn't fling much after you apply it.
Alright, now that the chain has been warmed up from your quick ride, it's time to lube it. You don't want much lube flying around and getting on your rear tire, so spray the chain about halfway between the front and rear sprockets. Spray a 6-8 inch section, making sure to get lube on all 4 sides, but mostly in the top and bottom. Then either move the bike, or roll the back tire to get to the next section of chain. Repeat until the entire chain is done.
Once the entire chain is lubed, and if your using a rear stand, then there is one optional step that I do. Make sure the rear stand in very stable, then start the bike, put it in first, and slowly let the clutch out. The rear wheel with be spinning while the bike idles. Spray the chain in the same area and let the chain move under the spray. Maybe 10 seconds of this just helps get a pinch more lube in there. Turn the bike off.
Now wipe off the excess lube with a rag, and let it sit for about 15 minutes. Then go for another 1-2 mile ride to fling off the extra, if any. An all out ride is fine too, as long as there is some riding after the lube is applied.
The best time to inspect a clean is right after it's been cleaned. While your going through all the steps, look at the chain for any cracks, bends, frozen links and such. Once cleaned up, look again. At this point your going to want to inspect specifically the rollers in between the side plates. They are the little round pieces that the sprocket actually rolls against. On a good chain, you should be able to roll them around with your fingers. As a chain ages, some will get stuck. If go by the 1 in 10 rule. If more than 1 in every 10 links has a roller that wont spin, then I'll start looking into replacing the chain. Some people use a 1 in 5 rule, use your own judgement.
Part of chain inspection is checking the chain tension. You'll want about an inch and a half total slack on the chain. Put the bike in 1st gear and creep it forward a pinch to get tension on the top half of the chain. Then grab the bottom half and move it up and down. Should be a total of 1.5 inches. If its too tight then it will strain the chain itself, rear sprocket, front sprocket, transmission out shaft and etc. Most people dont realize that as the rear suspension moves up and down while riding, then chain changes tension as the rear sprocket moves farther and closer to the front sprocket. While yes, it's an up and down motion, the distance from sprocket to sprocket changes slightly. It's generally the closest at 50% shock travel. If the chain is too tight or too loose, check your manual on how to adjust the chain.
Most bikes have some sort of indicator on the swingarm or chain adjuster to let you know if the chain is so old that is has stretched beyond acceptable levels. Another way to tell is when you run out of adjustment and the chain is still too loose.