I'm totally confused

Did you check for spark once you got back home?
How does the compression feel?
The poorly reassembled muffler? Did the end cap come off or did it come loose at the cylinder?
Can the engine start and run at idle? And if so, does it free rev or just bog down when trying to rev the engine?

the reason for the questions is because it could be one of a few things.... it could be as simple as your head worked it's way loose and needs to be re torqued, which will cause a loss of compression bad enough to prevent it from starting, or if it does start it'll just bog down when trying to rev the engine.

If the exhaust came loose at the cylinder and you kept riding it, this could be bad because the cold air can get sucked into the exhaust port and distort the rings or even worse, melt part of the piston. Luckily, pistons and rings are cheap for these and easy to replace.

If it's not getting spark, then we need to first look at the plastic boot on the spark plug wire, these are notorious for failing, and also look at all your wiring connections, they need to be firmly connected and the terminals need to contact the wire, sometimes the culprit is a bad wire terminal that wasn't crimped down tight enough and you got a loose wire making and breaking contact, or it was crimped too tight cutting the wire so it only contacts intermittently. Check that all the contact terminals are insulated or wrapped with electrical tape etc... a bare terminal can slap against the frame shorting out the power from the mag to the cdi. Another common issue is the ground wire on the magneto, make sure it has a good contact to the metal core on the magneto, these are coated with varnish at the factory and sometimes that thin layer of varnish is enough to prevent a good ground contact, and the blue wire has been known to come un soldered from the coil which will prevent a spark.
Also, if the mag coil got wet it's gone.
Check your head nuts to be sure they didn't work loose, check for spark, then check compression if you got a compression tester, you can also check if the engine has a good resistance to turning over with the mag cover off and using a 14mm wrench to turn the engine over, it should have a decent amount of resistance then go easy as it turns over, if it turns over real easy or you can turn the mag rotor by hand without a wrench it's possible you lost compression either from a loose head nut or a scratch in the cylinder bore... cylinders are cheap too so not too much to worry about, but do all the basic checks, spark, compression, and fuel delivery, then get back with us if you don't find the problem.
Also, pictures help a LOT when troubleshooting in here

sounds like it may be really rich - before changing needle settings & suchlike, be sure the bottom of your motor isn't full of fuel

This sounds like a timing issue to me. I know in cars when you upgrade to a high compression head, you have to switch to a fuel with a higher anti-knock index. Otherwise the fuel detonates before the spark occurs. Try using 90AKI fuel or higher if you're not doing so already. Also, you could try a spark plug with less resistance like an NGK. That will advance the spark timing slightly.

P.S. I'd recommend a 40:1 mix ratio regardless of break-in stage. That should be about 6 and a half ounces to 2 gallons. http://www.csgnetwork.com/oilfuelcalc.html

That does clarify things a bit... If your plug is wet and oily then I would check the carb and make sure the float isn't stuck, this can sometimes be detected by turning the fuel on and waiting a minute or 2 to see if you got fuel coming up out of the carb... or wait about 15 to 20 minutes and see if you got a puddle under the bike...
Seriously tho, it does sound like maybe a sticking float or some trash got in the carb and is keeping the needle and seat valve partially open. It could also be the main jet came loose and fell out which would make it run way too rich to keep going or to even start, this usually doesn't happen but if they just put the jet in finger tight at the factory and didn't snug it down it could fall out with the engine's vibration.
I would also mix up a batch of 32:1 and run that mixture if there's oil on the plug. 16:1 is way too much oil, even for break in, most of us break the engines in with 24:1 or 32:1 then run them at either 32:1 or 40:1.
Check your spark plug gap as well while you got it down and set it at .024 to .026", these ignitions aren't that strong and most plugs come gapped a lot wider which makes these engines hard to start.

It could be... has your fuel been sitting in the tank for any length of time? The gasoline these days tends to go bad a lot faster now that every place we buy it it has 10% ethanol in it. It'll last ok for about a month or so but tends to go bad since the alcohol can absorb water and the alcohol also tends to break down which ruins the fuel.
It could also be too much oil in the mix, then it fouls the plug until it can't fire. If the plug is covered with oil it won't fire because the oil is less conductive than the air gap. You can clean an oil fouled plug with carb cleaner if it's not too bad but it's also just as easy to replace it if it's really bad with a layer of black that won't spray off with the carb cleaner.
If your fuel mix is more than a month old I would throw it out and make up a new batch and mix it at 24:1 or less... these engines tend to like a mix of 32:1 to 40:1 depending on your riding style. 40:1 is usually ok, but if you live in a really hot environment and ride it hard, then 32:1 will be better.
Even 20:1 puts too much oil in the mix which can also lead to overheating since there's less gas going thru the jet to cool everything, now if you jetted your carb richer to compensate for a more oil rich mix it would be ok but still rough on the plug.
At 32:1 with the stock jetting it should leave your plug a dark tan color and it shouldn't be oily at all.
Also remember these ignitions aren't that strong so running a tighter plug gap can help with starting and running since too much gap culd prevent a start or cause miss firing under load. If you got a high compression head you definitely don't want a gap larger than .024" since the higher the cylinder pressure, the harder it is for the voltage to jump across the gap, but closing it a little will usually clear up the problem.
You may feel that when accelerating when it starts to get into the power band it'll start to miss intermittently and it feels and sounds like it's 4 stroking so people can mistake the miss for 4 stroking at these rpm's where the engine would normally make the best power. If this is mistaken for 4 stroking and someone leans out the jetting it could cause overheating. This is also why you hear people saying the 4 stroking went away after they installed an upgraded ignition, it was never truly 4 stroking, it was just breaking up in that rpm range and the stronger ignition let the spark jump over when the engine reached its power band where the cylinder pressure is at its highest.

As for it not starting at all, it's most likely the oil fouled plug and bad fuel, whether it's too much oil in the mix, you got a bad batch from the gas station or the gas went bad somehow after it was mixed up, either by absorbing water from high humidity or just sitting too long etc...
Just make sure you got spark at the plug, drain the carb and replace the fuel for a fresh batch and it should start.

Did you check the exhaust for restrictions? Most the time the stock exhaust is self cleaning but if too much burnt oil and carbon crud accumulates in the pipe it could restrict it. You can try taking the end cap off and see if it still bogs or not, if it don't bog with the end cap off then the exhaust is the culprit and you'll need to find a way to clean it out really good. If it still bogs then it could be a really weak ignition or poor compression. I've lost compression before because of a bad set of rings and replacing the rings brought the power back. I was actually running just one ring at the time and it made some impressive power but then it started to get really boggy on me, I noticed it by turning the crank by turning the mag rotor with the cover off, I was surprised that it would turn over so easy then I took the plug out and ran a compression test. It was only making about 40 psi coasting it down the street with the clutch released.
Luckily it happened after only about 15 minutes of run time so I was able to swap the rings without needing to replace the cylinder or hone it out. If you lost compression because of bad rings, you can still use the same cylinder but it'll most likely need to be re honed if the cylinder wall is glazed and really shiny.
Another thing that could cause a compression is damaged plating inside the cylinder, this isn't uncommon on these since sometimes the plating will start to peel and flake off from around the ports. It could also have a scratch in the cylinder wall from something getting in past the air filter like if you live and ride in a dusty environment it's possible something could have got thru and scratched the cylinder wall, the only real way to check this is to pull the head and look down into the bore with the piston at bottom dead center.

This is worthwhile to check if you got good fuel and spark, if you have a compression tester I would check the compression, the stock compression should be above 90 psi and with a high compression head it should be about 130 or so. You can usually borrow a compression test kit from auto zone or O'Reilly auto parts if you don't have one, or you can borrow from a friend if they got one.

Yeah, the end cap has a really small outlet pipe and it can clog up with crud and burnt oil etc, but also the pipe it's self just has holes drilled thru it and the end welded shut with the bolt for the end cap welded on so taking off the end cap won't completely reduce the restriction, but will reduce it enough to make a judgement call.

When the other pipe gets there and you get it installed you should see a good difference and the engine should clear up some more, but it still might need some minor tuning. You got it this far so the rest should be pretty easy.

Good to hear you found the problem