[The machine stops (followed by white smoke!)]

The problem is you never know what the engine mariniser fits. For safety reasons it should be energise to stop, but some of them stick with the industrial standard which is energise to run.

[The machine stops (followed by white smoke!)]

Could it possibly be a fault with the stop solenoid. Maybe failed, burnt out causing smoke and engine to stop. Not sure which way the solenoid works on this engine, energised to run or energised to stop. 

[Question.. Not sure how to title this.]

No it is not normal. There is no gasket or anything like that but it looks like when the cowling was fitted the bottom edge has caught on the crankcase. Ideally it should be removed and correctly fitted so you dont lose too much of the cooling air through the gap.

[Lister sr2 engine oil and fuel filter change.]

The black handle shown in the second picture looks like it is the sump pump to drain the oil from the engine. Just check a pipe comes from the bottom of pump and goes to the sump. In the first picture showing the dipstick it is showing way too much oil in the engine. There are 2 marks on th dipstick which relate to maximum and minimum levels. The number 8 on the dipstick is just the Lister identification mark. As far as the oil goes you should be using a low spec (API CC) mineral oil. The fuel filter has a bolt on the underside of the bowl which when unscrewed will allow the bowl to be removed and give access to filter element. The system will need bleeding. If you are lucky you will get away with just bleeding at the filter unit with the small bleed screws on the top. If unlucky you will also have to bleed at the fuel injection pumps.

[Lister Engine Belts]

I think originally the engine would as standard have an alternator mounted onto the flywheel guard. With this in place there would not be a problem as the alternator would move to allow belt tension.

[Starter motor studs]

The studs will be 3/8 UNC/UNF from memory