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Your shift fork set up is correct. Mama Kawa made a mistake and switch the numbers in the manual pic F69.
Take a look at the pic F63 (#52->5th and #58->4th gear) and pic F78 of the 4th/5th gear position on the output shaft.


 
 

Thank you for that observation.  I missed that illustration of the transmission.

I finally managed to get the engine components vapour blasted last week.  No excuses now for not proceeding with this rebuild.  The photo below shows the engine with the cleaned parts in correct position but not actually installed.  It's been so long since I disassembled everything that I've forgotten where I put some of the smaller parts.  Luckily everything was bagged and tagged, so my only issue is finding the bags.  Most are in one bin but a few went into other locations.

Yesterday I put the pistons on and slid the cylinders over.  In the past I've always done it in the frame but this time the engine was sitting out of the frame.  Much easier!  Maybe it's because it's a 650 but I was able to wiggle the cylinders on top of the pistons until they just slid into place.  Today I started to put the valves back in.  I'm lapping each one as I go and then installing when I have both valves for each cylinder ready.  

 

Another project bike?  I picked up this D2 today.  When I first saw it I thought it could serve as a donor for parts I don't already have.  But when I looked closer I realized it was actually a better restoration candidate than my first one.  Everything is there, and in reasonably good shape.  I have no idea about the engine as I wasn't concerned about its condition because I already have one.  I need to do some serious checking tomorrow...will post a few photos then.

 

I usually find a mystery or two while pulling an old bike apart.  This is the first one for this bike.  The gauges have chrome covers over the top half.  When I pulled the cover off the tach I discovered that someone had been into the guts, but when they pulled the ring off the center of the gauge they must have destroyed the ring, because there was none visible when I checked it out.  So their fix was to install a chrome cover with the chrome ring that holds it in place.  Great idea, but not so good for preventing moisture from getting into the gauge innards.  I have a spare Z1 tach that I'm thinking of using instead of this little beauty.

Z1 tachometer will be black around the perimeter. The 650 is blue. Won’t match. 

wrote:

Z1 tachometer will be black around the perimeter. The 650 is blue. Won’t match. 

That's correct!  Originally I was going to put an entire Z1 front end on this beast.  That plan changed when I realized the brake pods from a 650 had a different mount spacing.  So I decided to go with the Z1 triple tree but I effed up one of the upper pinch bolts....broke it off in the hole.  So I had to order another top triple mount.  Progress is halted until it arrives in a couple of weeks.  Meanwhile I can pull components apart and clean them up.  

I guess I'll try the tach as it is.  If it doesn't work I'll buy another one.
 

Currently rebuilding the front brakes.  What paint should I use that won't peel off from brake fluid contact?

That's easy, don't get brake fluid contact. Always keep a wet rag and some water handy when doing the brakes....

FWIW, I use VHT Caliper paint. I mention earlier, to me it was untested, but I forgot I used it last spring of 2020 when I detailed the rear of my ‘78 1000 B2. I bled  the rear brake, I’m sure I got something on it. I had a rag handy but wasn’t aware a wet one was better. So far two riding seasons and no failure. And that was before I knew heat curing is recommended.

I should have added , I use VHT caliper paint too, then bake it in the oven, baking the paint helps with hardness but won't eliminate brake fluid damaging it f fluid is left on the part.... Brake fluid will ruin most paint if left on it, that usually means a leak. Use a clear tube over your brake nipple and put the other end into an old bottle when bleeding, keep fresh water handy. I've bled many bike brakes and never ruined the paint....

I've been stuck for a long time trying to get the swingarm bolt out.  I finally had to get a shop to cut it out, so things are beginning to move a bit.  Frame painted on the weekend.  Engine in the frame today.