Honda-SOHC

Not sure going to Black is going to help.
You’ve posted two sets of readings and got different results, so not consistent readings.
Set 1         0.050mm 0.050mm 0.050mm 0.038mm
Set 2         0.038mm 0.050mm 0.050mm 0.025mm
Are you giving everything a clean between readings? No remanence of oil, plastigauge or anything else that may affect your results.
Conrod and cap aligned with the C and 2 always matching?
Conrod installed with shell tabs to the exhaust side?
Torquing progressively on both bolts i.e. not torquing one up then the other?

The Cs on the conrods are the weights, the only thing that matters about that is they are all the same.
Take the As from the webs and your conrod shells are A2, A2, A2, A2 which is Yellow.
Using Green or Brown should give you tight tolerance. Are you just tightening them or torquing them?

https://www.rsbikepaint.com/en-gb/colours.php#makeid=66&modelid=2105&prodyear=1975&colourscheme=3963

This is a list I started to put together a while back. Can't remember if it's complete or accurate but may help you putting your list together.

Diagram      Part No.   Description                            Quantity
Gasket Set            
D1   107   16173-253-004   Carb insulator O-ring 27 x 2.4             4
C1   277   91302-001-020   Tappet cover O-ring 30.8 x 3           8
D2   18   12209-333-005   Valve stem seal                                   4
C2   31   12909-333-000   Cylinder stud seal                           2
C2   32   12910-333-000   Oil orifice seal                                   2
C2   276   91301-377-000   Cylinder base O-ring 55.5 x 2           4
C2   14   12191-377-000   Base gasket                                   1
C1   19   12251-377-000   Head gasket                                   1
C1   24   12391-333-000   Rocker gasket                                   1
C1   22   12329-333-010   Breather gasket                                   1
C1   275   91301-333-000   R oil way O-ring 7 x 1.7                   1
D2   280   91305-333-000   L oil way O-ring 5 x 1.7                   1
E1   8   11394-377-000   Clutch gasket                                   1
F2   9   11398-333-020   Sump gasket                                   1
G2   12   11691-333-000   Alternator gasket                           1
Oil Seal Kit            
A2   265   91201-300-003   Crank oil seal 30x42x8                   1
B2   266   91201-323-005   Crank oil seal 30x45x8                   1
C1   267   91201-324-010   Tacho oil seal 6.5x14.5x7                   1
E1   268   91202-216-005   Clutch oil seal 14x24x5                   1
E1   269   91204-259-000   Kick start oil seal 16x28x7                   1
H1   270   91205-333-005   Drive shaft oil seal 34x52x13.5x15.5   1
H1   271   91206-286-005   Gear change oil seal 14x28x7           1
H2   272   91207-333-000   Mainshaft oil seal 34x9                   1
Oil Pump O-ring Kit            
H2   278   91302-044-010   Oil Pump O-ring 6.9 x 1.5                   2
H2   279   91302-377-000   Oil Pump O-ring 15 x 2.5                   2
H2   215   41123-516-00   Oil pump O-ring 63 x 2.5                   1
Separate Items            
B1   45   14401-333-003   Camchain                                           1
G2   140   23131-323-000   Primary chain                                   1
G2   139   23114-323-000   Primary drive damper                           8
E1   238   90431-292-000   Washer.Lock 16mm                           1
G2   239   90433-283-000   Washer.Lock 6mm                           1
H1   240   90435-333-000   Washer.Lock 8mm                           1
F2   287   91329-590-003   Sump filter O-ring 16.5 x 2.8           1
C1   242   90442-377-000   Seal Washer 18od x 2.2 x 8mm thread   2
F2   283   91315-044-000   R main oil way O-ring 19.4 x 2.8           1
F2   286   91319-300-000   L main oil way O-ring 13 x 2.5           1
F2   282   91314-220-000   F main oil way O-ring 16.4 x 2.4           1
H1   213   35751-333-003   Neutral switch O-ring 11.2 x 1.8           1
A2   285   91317-703-000   Camchain adjuster O-ring 6 x 1.7   1
C1   30   12905-333-000   Oil pipe holder                                   2

Have you made any progress with the permanent taillight?

You say you have checked the connections at the taillight and that they are ok. These connections are from a sub loom, have you checked the connections at the other end, under the seat?

Not sure it’s possible to connect the black feed to the brown taillight feed as the connections should both be female but it’s worth checking (in the head light bowl).

It is worth checking the function of the ignition switch but in my (limited) experience problems with the ignition switch usually lead to things not working rather than working when they shouldn’t.

The taillight works separate from the head lights and is powered with the pilot light (small separate bulb) in the head light bowl. Is the pilot light on when the taillight is on?

Is the pilot light bulb ok?

Does the taillight go off if you disconnect the front or rear brake light switch?

Are the speedo and tacho lights working ok?

An easier mistake for someone to make would be to cross connect the brown and brown/white connectors in the head light bowl.

Lot of questions but as Bryan says it’s not easy to diagnose electrical issues at a distance.

Not sure what work was done on the bike and whether there was any reason for anyone to disconnect any wiring unrelated to your engine refurb.

Dave,

I don't know how reliable this site is but they give the following code:  Color Code: Y-31   No. QE   Color Code Name:  Parakeet Yellow

https://www.motorcyclespareparts.eu/en/honda-parts/honda-color-codes

Hi Ash.

Will need a clean, bit of heat and gentle persuasion to get back into shape and then plating. If you want it, PM me your details and I'll get it in the post.

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When you say the clearance is 0.01124, do you mean the crank measured 31.98876?