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Looking forward to seeing your reports during your rebuild

What KB said. Always on the look out for good high quality gasket kits. Especially head gaskets 1st overbore. 

Tonight I couldn't sleep and I decided to go for a while to start disassembling the motorcycle.

After draining fluids, removing the radiator, coils and cylinder head cover, it occurred to me to take a set of gauges and measure the space between the distribution shaft and the valves.



I have been rotating the crankshaft looking for the timing points to find the valve crossing as indicated in the workshop manual.
This is the result:
Cylinder 1:
Intake 003
Exaust 007
Cylinder 2:
Intake 003
Exaust 008
Cylinder 3:
Intake 004
Exaust 008
Cylinder 4:
Intake 005
Exaust 006
Cylinder 5:
Intake 001
Exaust 010
Cylinder 6:
Intake 007
Exaust 009

Cylinder 5 has low compression and uses oil, the intake valve clearance is minimal, 001, but the valve does not appear to be depressed, the shim turns with a finger.


My question is this:

Are those space tolerance values ​​correct?

Should I assemble everything the same when I restore the cylinder head?  

As per the Factory Service Manual
Intake should be .05mm - .15mm  (.002-.006")
Exhaust should be .05mm - .25mm  (.006" to .010")

When adjusting the shims you want to aim for the highest tolerance because as the valves wear, the tolerance will tighten up.
So adjust the intake to .15mm (.006")   Knowing that shims come in .05mm (.002") increments, I would not adjust the intakes any tighter than .1mm (.004")
Adjust the exhaust to .25mm  (.010")     Knowing that shims come in increments of ,05mm (.002") I would not adjust the exhausts any tighter than .2mm  (.008")

I spent this Sunday disassembling the motorcycle.
I already have the engine half open.

At first glance the primary and secondary chain are too loose, I have to change them.




The problem I have is that I don't know how to find the timing mark on the crankshaft, the teeth are worn, the mark on the secondary shaft is clearly visible.

 

 

 
The next step is to order the spare parts, I have found a German website that has them available.

www.z1300.de/

As for the timing mark on the crankshaft, I would suggest you get the secondary shaft in position and then count forward 7 full links and you should be able to see the mark on the crankshaft and confirm it. Then if necessary re-punch the mark or put a score line on the crankshaft so you know which tooth to use for alignment.

Looks like you made a good decision to replace the primary and secondary chains. I am surprised that they needed to be done. Maybe the previous owner used cheap oil. Some of us here are partial to Shell Rotella T6 15W40 . It's actually a diesel motor oil but it has the MA and MA2 ratings for motorcycles. The zinc additive they put in it for the heavy duty diesel engines is excellent for wear resistance. The MA and MA2 rating for motorcycles is a rating to identify oils rated for use in engines that also have clutches so these oils will cooperate with the clutch pack regarding shifting and slipping.