I'll be the baddy sorry & i know you've got good ideas so "stick with them".
But those & earlier design 360's have a "steel ring" in the crankcase & i just press the bearing in oiled & cold usualy.
On the left i think you'll find they run an "extra internal clearance bearing" because the crankshaft is very tight in the bearing therefore its trying to expand the inner race & at the same time the case ring is compressing the outer bearing shell.
The extra clearance is in the ball race fit where the balls run & not outside or inside case or shaft fit.
The right bearing doesn't require that clearance although it wouldn't hurt if it did & might allow something for slight misalignment.
Right side crankshaft is a sliding fit into that bearing & the fit is designed into the shaft size not the bearing, & shaft is likely a thou smaller than the mag side.
& like i said earlier the clearance on the left side bearing is in where the balls run not the shaft size bore of the bearing.

Happy to be roasted over this.

Just re-reading--freezing your bearings might drop them in just like that with little pursuasion.
If heating the case ring too hot you might see oil at the ring edge as i think its cast in but doubt it'd hurt it.
On the older models like mine i've never seen one of those rings come loose on 250 or 360.
Might find it easier seeing you're freezing things, to drop the frozen crank into the left bearing because the right side just slides home providing the shaft is clean.
Don't take too much notice of me.
Edit--to top that off i just looked at partzilla & both bearings are the same part number so "i don't know" anymore-sniff sniff.
If its a C3 or C4 bearing it'll be etched onto it.
www.partzilla.com/catalog/yamaha/motorcy...0a/crankshaft-piston
Double edit lol--Here's a pic of the bearing & i can see "C3" on it in the pic so looks like they preffer extra internal clearance both side, so i'm kinda on the right track. Sleep well!!.
www.partzilla.com/product/yamaha/93306-3...04fb154d07cb409557dd
Also i thought the A model ran smaller OD crank bearings than the older design model RT-DT but both models say 6306 so must be just the seals smaller od. I live & learn.

Heating isolated areas of the case with a torch is not something I'm too fond of...  Best way I've found is following the manual.  Freeze all the bearings.  Heat case half in oven.  Install all bearings in the case half as quick as possible.  Repeat with other case half.

I tend to leave crank seals out until very last which is may not be the best way, easier to get them in before the crank. BUT, this depends on your crank install tool.  The one I made bears on the inner crank bearing race so seal on ignition side must go in after cases are together. 

Since you have the install tool, I would not even consider the "freeze crank, heat bearings" thing. 

As RT325 said, crank should drop into R (clutch side) crank bearing.  Secure with the nut and gear.  Get the trans in place.  Apply Yamabond. Then install the left case using the install tool.  Done.

Don't forget to install crank shims if your bike had them!

I was wrong. It appears that I have a Tusk crankcase separator and crank install/uninstall tool. From what I can tell the tool will pull the crank through the mag side but doesn't appear to fit the R side for "pulling".

Right side doesn't need pulling as its a snug push fit into the bearing unlike the left side.
Maybe get some fine emery paper or wet & dry & just give the right side shaft a wipe around with your hand just be sure its clean.
If ya not sure of this just get the old bearing--[or new one if its not in the case] & oil it then slide it on the shaft so you then know how it fits.
& think Mark said don't forget any shim that might be fitted but i'm not sure they run one in your year. Parts listing should show--or not show as case might be.

@PABDT: found this thread because I have to do exactly the same work on my DT360A! A lot of tipps which will help to bring the DT in a nice condition like new A lot of parts have been still sand blasted and waiting for primer (up to now not the weather for painting metal in Germany). Motor is disassembled and now I´m waiting for spare parts (bearings, sealings.....). Good luck for your project. You are a lot of steps ahead... :(

Is the VIN sticker a reproduction? Where have you purchased it?

well,  I've been slacking a bit the last year or so but I'm hoping to get the project quickly done now. 

I got the reproduction stickers from DEET a forum member on this site. 

This bearing doesn't look correct. No snap ring on it from partzilla and its got I guess what appears like an anti-roll ball or alignment notch?

I don't have the original bearing. Please check the pics out and let me know what you guys make of this.

Is for L case, sprocket drive axle.

I believe that's a TZ crank bearing...  it's been discussed on here before that Yamaha had an issue with a bearing part number.  It's not correct as you probably know.

I didn't find the post but I found an old parts list. 

Bearing is supposed to be a 93306-30517-00.  Partzilla has them.  It's a special bearing with snap ring and a special edge radius so best to get it from Yamaha unless a bearing supply has a 6305X1N...  the "X1" is the special radius designation.

Partzilla bearing on ebay link