I can only speak to US models but it looks like there are parts off of different years. Every Yamaha I've owned has the stamped VIN numbers on the right side of the neck. Steering locks were introduced in the '72 models. Engine covers are off a ''70 or '71, YAMAHA logo was recessed in '72 and '73. Exhaust pipe is from a '72 or '73 judging from the heat shield. Heat shield was different for the '70 and '71 and the mount locations were different. I'm just a rookie at this and I'm sure smarter people will weigh in but if it were me I would get it running and enjoy it.
Cheers

I’ll have to check out my flywheel again this evening! I may have overlooked something. I will say the flywheel but was on there pretty good when I took it off to clean the points, and the key looked good too. I would be working on riding it tonight if I could but I’m missing a gas tank and want some seat foam for it so I’m in the market for those right now. 

As for the mismatched parts, that’s why I came here! The exhaust is definitely a ‘72-‘73, but the engine is definitely a piston port ‘70-‘71. As for the frame who knows, but I agree with y’all! I’m not gonna worry and I’m just gonna get it running and ride it!

The frame appears to be a 1970 vintage because there is an ignition key mounting tab located on the left side below the steering neck, the side mounting tab was not present on frames built after 1970. The gauge set on yours is from a '72-73, and includes the newer style ignition key switch between the instruments, evidently an owner in the past has replaced the gauge/key assembly.
The front forks are also 1970 vintage, for 1971 and up they were changed to aluminum lowers. The engine does look to be 1970-71 model. The chain guard is 1972-73, '70-71 version chain guard is much larger and mounts with 3 screws as opposed to 2 screws on yours.
As previously pointed out, the exhaust pipe is 1972-73 as well.
I would agree it is likely that your bike was originally produced for a non-US market (JDM), thus the VIN number out of typical range and the RT1 stamping on engine case without sequential VIN digits.

Was perhaps the bikes back then had a whole bunch of stuff made before they were’d assembled… then, sumptin new came out and the older stuff sat on a shelf… until, we’ll we need to get this bike out to supply the demand and the surplus was utilized?
Sneezles61

Thanks for the reply House of Enduro! I was just working on it and was wondering about the tab on the frame.

I have also discovered another interesting thing on this engine, the shift shaft appears to go all the way through the engine. I’ve never seen something like that! Has anyone else? 

I will say the bike is cleaning up very nicely! 

I learned on this site it’s for right side shifting probably for flat track use, I asked this same question when I started restoring a 70 DT1. There are probably posts about it in the forum including when I asked the question, 

Awesome I’ll go look for them!

I'm not going to contradict anyone that has said that parts from later models have been fitted. However, I would observe that, very often, JDM bikes got newer parts before anywhere else in the world, sometimes even intermediate models. To see an example, check online for photos of Yamaha RX models - 250 and 350cc bikes that came between the DS7/R5 and the RD250/350 and were, I believe, for the JDM only. They have parts that weren't on the DS7/R5, but were on the RDs.

Shift shaft is normal feature on early bikes.... it was about 1975 when the USA finally standardized left-side shift by refusing to allow new bikes with right-side shift into the country.... the trend towards left-side shift started before then.

So many bikes being sold in the 50's, 60's, and early 70's had right-side shift (For example, pretty much all the European motocross bikes had right side shift when the DT1 came out in 68.) that I believe Yamaha decided to offer their kit to convert to right-side shift for purchasers that wanted it... it doesn't seem it was a popular option as you rarely see one and even the extended shift shaft was phased out by Yamaha in the early 70's.

It could also be used for flat track racing, but again, conversions are rare.

A couple of things as you work through what you have.
Appears you have an RT1mx head on a 71 cylinder - has decompressor (not sure if this was introduced during the 70 model)