Takes a brave man to admit his mistakes & great you found it. Best thing is you descovered it yourself. Look forward to good news--running--& as MarkT says, hope right side is fitted. Wouldn't go dismantling to check the right side yet, just fix the left & you'll know straight away.

Well I have good news and then some really bad news. The good news is that the missing crank seal was the problem. I was able to finally get it started. Everything was going great. I ran it for about 5-10 minutes while I adjusted the idle and mixture. I then decided to take it around the cul-de-sac. Everything was going great in 1st and 2nd gear. When I shifted from 2nd to 3rd the bike died. I started it back up and there was a metal rubbing sound. Right away, I knew something was wrong. It will run, but it sounds terrible. I pulled it back into the garage. At first, I thought that the oil pump wasn't working and the cylinder dried up. Turns out that wasn't the problem. I drained the transmission oil, which was brand new, and it definitely has metal in it. It's very dark and you can see metallic specs. I am devastated. This has been an on and off project for 2 1/2 years. I guess I have 2 options at this point. I could either pull the engine and investigate on my own, or take it to someone who actually knows what they are doing and have them rebuild it.

I really hate to see this happen to you. Frankly though, if I were you I would pull the right side cover and just start looking around. Maybe it's something to do with the clutch not being assembled correctly, or maybe it came loose, or who knows? If you didn't have the right side seal in well, the transmission oil could have been contaminated with two-stroke oil, which would make it darker. In any case, I would definitely investigate, before you try to find someone that will work on it for you. I wouldn't assume it was anything catastrophic yet, you never know.

I had what sounds like the same thing happen on a fresh build I did a couple years ago. Turned out to be the nut on the primary gear came loose, I guess I didn’t get it tight enough. Took the clutch cover off, zapped it real good with a half inch electric impact gun and never had any more trouble with it 

I agree, don’t panic, just clean up, take a break then come back to it.  Very possible something is loose or rubbing.  

Thanks for the encouraging words guys. I was already thinking it could be something with the clutch. I'll pull off the clutch cover today and see what I find. Fingers crossed......

Usually at least with me when I have a similar issue and go in expecting the worse with doom & gloom it turns out to be an easy or cheap fix and I feel lucky. On the other hand when I think I know what the problem is and thinking it will be a easy and cheap fix, it turns out to be a disaster that will cost a lot to fix and will take hours and days to fix, usually with a broken off or stripped bolt thrown in for me, on what I thought would be a 15 minute job.
Good Luck on it being a simple fix, we have our fingers crossed for you.

R578.
The reason it wouldn't start is because you had very little fuel charge and no crankcase compression. Effectively, the combustion process was open to atmosphere as there was no gas seal.
Don't forget the O ring on the primary drive side crank end if you check that side out. Without that you have the same thing and ingress of gearbox oil. You would know soon enough if you missed that one.
Good you found it and admitted it to your self.
By the way the bike looks nice . 
Find Micou Meekoo on youtube and his red 175 tearing around the mountains in France . Great to see that little bike in action.

I pulled the clutch cover yesterday and everything in there looks good. I did not forget the crank seal on that side and I remember installing the o-ring at the time. I did realize that I had installed the clutch plates in the wrong order. I started with the friction plate instead of the clutch plate. I fixed that, but I'm pretty sure that was not the problem. The transmission was in neutral and everything was spinning smoothly, I did not feel any grinding going on. I was able to tighten the bolt on the primary gear about another quarter turn. I think the transmission is okay. After playing with it more, I realized the noise is coming up out from the intake. I used a crank seal from a 77 IT175 like Mark said. When I installed it, I could not get it to seat flush with the outside of the case. I was using a wooden hammer and an oversize socket. Not sure if that is how you are supposed to do it, but I was hitting it pretty hard trying to get it to seat all the way. I'm wondering if it was actually too think and I somehow unseated the crank bearing all the way. I was noticing a squeak right away after installing the crank seal. I am afraid I have somehow damaged the crank bearing. At this point, that makes the most sense. I actually have the crank seal that I forgot in the first place from the rebuild kit. If I remove the one I installed, would it be okay to squirt some 2 stroke oil or something like that in the crank bearing and see if it could be saved? Install the new seal and see if it goes away? I know that sounds a little crazy, but I really don't want to have to pull the motor and split the case again.

I wouldn’t worry about ruining the crank bearing solely by driving in a seal from the outside because the bearing is well protected within its bore on the other side of the case.  The only way you could hose up the bearing from outside is if you somehow whacked the cage / balls from the outside IMO.  How far above case is the top of seal?   I’ve whacked these in with a socket, a pvc fitting and also pressed in with a crank puller which works great on bench. 

might want to check stack up of thrust washers etc under clutch basket and between basket and hub to make sure everything is in correct spot. 

the one time I had a terrible noise after assembly was on my dt400e that would make the absolute worst noise that got worse with clutch pulled in.  It turned out that the bushings on 1st and 2nd gears that ride on the clutch shaft were burnt out.   I ended up buying a complete transmission for $40 and problem solved after a complete redo, including re cleaning mating surfaces of yamabond which was a pain in the ass.  But the results yielded a great bike, which you will soon have!!!