Jens,
You should set both cylinders at the same timing, then perform you evaluation. You also need an infrared heat detection gun to fine tune the fuel delivery and match the exhaust temperatures in both cylinders when under load.
In the past I designed many high performance engines (diesel and gas), first I figured out what the application was and then I design my own cam grind (lift, duration, valve overlap, ramp speeds, ect.) to meet the set requirements, then have it cut to specs. Camshafts are like pump injection timing on diesels, they only operate at optimum efficiency in a very small rpm range. This optimum range works great when working on generators with their fixed operating speed. As to an automotive engine that needs to operate efficiently at a wide range of operating speeds. Â
If a diesel  engine has an useful operational speed  between 1,500 RPM and 3,000 RPM for instance, the proper pump setting would be configured to 2,250 RPM. Anything above or below this operating speed is a “compromising” pump timing setting. Maximum cylinder pressure has to be set at 5 and up to 7 degrees ATDC for maximum power and fuel economy. This enables the proper rod to crank angles for maximum burn rate and mechanical leverage. The further down the pistons travels the greater the mechanical leverage but at a much reduced downward force from the thermal expansion. This brings me back to the heavy flywheels on the engine and on the generator.
You can retard the timing more on an engine with heavy flywheels than on an engine with lighter flywheels. Case point, when an engine with heavy flywheels approach TDC the fuel is injected 2 degrees (approx.) later than an engine with light flywheels. This would display a smaller deceleration effect on the crank due to it is compressing a smaller thermal expansion effect than on an engine that is injected 2 degrees sooner. Now, after TDC the heavy flywheeled engine would stay closer to TDC longer (so it could still achieve proper burn rates) than the light weight flywheeled engine because of the stored kinetic energy potential is higher. The light weight fly wheeled engine would “crack” ATDC and the piston would move further down the cylinder per given time frame.
Your valve train would receive reduced sudden shock loads as well with mild timing, which is a problem in these engines. The reason behind all this is that even the slightest reduction in pump timing can dramatically increase the engine operational life and provide better quality electrical output.
To achieve optimum pump timing at a certain engine speed, load, fuel ect. , I’m afraid you are going to need to take the heads off periodically to see if you are producing too much carbon buildup. If this happens you should slightly advance to achieve a suitable amount, or add a constant DC load to keep the combustion temperatures in a suitable range. The key is to have the engine still perform as it should with minimum pump timing to achieve your goals. It sounds like a lot of work but it is time well spent, you will have a smooth long lived engine.
This is what an engine sounds like with conservative pump timing and it could be close the same timing as conventional 6/1 but has heavy flywheels, you would need to know altitude and BTU content of the fuel to directly compare this to other engines:
http://video.google.co.uk/videoplay?docid=-5803127844512609207&q=lister+start-o-matic&total=2&start=0&num=10&so=0&type=search&plindex=0If the belt chirping still persist, I would opt to a double belt system to increase traction on the flywheel without over straining the bearings with a single belt system. As BruceM mentioned, Lister had it right over a half a century ago with its dual v belt design, which sunk into the groves when the piston past TDC and then released.
Oliver90owner mentioned that you don’t need to be so precise and he is correct you can just mark where you are now and retard or advance from there. I’m a motor head and would pursue the exact timing but that’s just me.
Diesel Guy