You should use a set of callipers to measure the distance from the gudgeon pin hole to the top face of the piston.   Then it is much of a guess to tell which sticks up the most.   I had the trials piston which was flat, and a road piston which was slightly curved, and a Methanol 12:1 piston which had about a half inch of dome.

Remember that the total volume above the piston is only about 25cc, so every 1cc will make a big difference, and maybe push the CR beyond modern pump petrol.

If you do the porting to match the carb and a bigger inlet valve, measure the weight of the valve, to make sure the springs can prevent valve-bounce at maximum revs.   Stronger springs can give the problem of pulling the head of the valve ( not sure if this is more for the inlet or the exhaust.)

Having messed about with these sort of things in my youth, and made many mistakes, I would settle for stock these days.  I hated having to put the push rod tube back on..!

Getting back to the cam and valve opening discussion.   On the non power stroke at TDC, the valves will have an overlap, where they are both open a small amount. 

Racing cams have a large overlap of maybe 50 degrees each.  Road bikes have much less overlap, and lawnmower and industrial stationary engines have zero overlap.

The position where both valves are open the same amount is -nearly- always at TDC. and is a good way to check your cam timing.

It is so hard to do clutch adjustments over the internet, but I will give some important things to look out for..

Make sure the clutch springs are not coil-bound.  The nuts are adjusters, and should not be fully wound down, still making sure the outer plate lifts off squarely.

The gearbox lever adjuster should bear perpendicular to the push-rod, so as not to put any side load on the rod.  Use a combination of the clutch centre bolt and the gearbox lever adjuster to get this right.

Finally slacken any of these adjusters, or cable, to give 1/8 inch free play on the handlebar clutch lever.

Is it possible that you are tightening the Clutch Spring Nuts down too much..?   They should not make the springs 'coilbound', and should each be individually adjusted to make the outer clutch plate lift off squarely.

If you have a centre punch or small cold-chisel, you can put two marks at the junction of the distributer and crankcase.  This will be a reference point for further experiments.   I did the same with one bike, and found it ran best when the marks were just misaligned by about 1/16 inch.   But at least I knew where to reset it.

Bit confusing this...  First is the washer supposed to be first on the shaft, or second , after the clutch basket is fitted..?

Second, what are the two threads on the shaft..?  Does the nut go on the big threads or the small threads..?   There must be two sizes of nuts.

I think you are spending too much time fiddling with the timing, when it might be that the carb is not set correctly.   Do you use any twist grip rotation when kicking..?   Have you got the idle mixture set correctly..?   
My B40 will only start with zero throttle, and needs to run like that for ten seconds before I twist the grip, or else it stops.   I suppose I could make some adjustments to make it better but have not yet tried, as it runs ok when warmed up to temperature.

Just to be pedantic, you said...
Then

Just below this mark , file another mark at the distance the book says before tdc it should fire.
So, if it is 3/16" before tdc , put your lower mark 3/16" apart.

You would need to put the second mark -above- the first mark.   Making the length of wire 3/16 longer.

Also when kicking from TDC, try to extend your swing forwards, for the maximum kick rotation.

Hi all, I finally got my BSA B40 on the road, so thought I would give it a trip around the lanes.
Above a certain revs, it sounded as if the crankshaft was leaving the engine.   So when I got back after the 5 mile round trip, I inspected the engine mountain bolts... They were tight.   

So I looked to see if it had a cylinder head steady... it doesn't, but noticed the tank was touching the 4 head bolts.  I then adjusted the single tank mounting bolt to give 1/4 inch clearance to these bolts, and took it for another spin.   This time the rumbling was not so great, but still there.

Back at the garage I noticed the centre bolt had a large washer under the nut, which was touching the metal of the tank.  So I repositioned it to only bear on the rubber washer.   I hope this fixes the crankshaft noises, but have not yet tried it down the road.

Will keep you informed of any cure.

I see that your adjuster is almost out of threads, so at the limit of it's adjustment.
I would run it for one hour and the chain will stretch a lot.   Then it will be time to remove a link.
After the one hour run-in, the chain won't wear much for the next few thousand miles.

From memory, the C15 Amal was 7/8 inch diameter.  So this would need the 22mm or 24mm Mikuni. 
If you go to 26mm, then the inlet port will need grinding out for gas-flow,

The C11 s a tinplate case, with about 20 small bolts holding it on.

Yea, I tried some of Halfords best blue thread locker, and thumped the nut up real tight.   Then adjusted the clutch springs to lift off symetrically.   A short test ride later, and all seems good to go for our next VMCC ride-out to Bala in Mid Wales.

After looking at the Cush-drive, I realise that it is not adjustable,   So just tighten the nut up sufficiently, and it should not loosen.   There is no provision for a lock washer, or locking pin or wire, it just relies upon being torqued up enough.

I have a 1950 C11, and was inspecting the primary chaincase, and found the nut holding the cush drive was a bit loose.   I tightened it up by punching on the castlations, but could not find any way of locking that nut in position.   
Short of putting a blob of weld on it, is there a better way of securing it..?