Morning Richard,answers to your questions are as follows.
Engine acquired from fellow club member,one Dereck Fox Esq(Del Boy)106,000 miles,I heard it running,albeit not for long as the water pump had been removed for modification(still ongoing

)I wasn't too worried as I had planed to fit an electric one anyway,and since I have had it running it sounds just fine,with plenty of Compression and no unusual rattles.
Water Pump is from an Australian Company,(Davies Craig and is their EPB Model,) and pumps out 4.5ltrs a minute.(any idea what the Commander pump out?)
No Thermal control switch,just on/off switch on the handlebars.
Thurmostat removed and housing left open.
New Radiator had to be custom made 'cos the Commander one was too wide to fit between the sub-frame on the Triumph Fairing,10mm off each side,hight and depth as per orriginal.
Carbs off the Classic.New "O" rings on every orifise,carbs striped and cleaned.
Is the Thermastor? the little one with two Blue wires? located close to the Water Temp thermostat?if so the answer is yes,it is connected.
2 and a half ltrs in the actual rad,just over 4ltrs in the auxiliary tank(6 and a half in total)
The pump is located level with the bottom hose on the rad,and then a hose goes from the pump to the top of the aux:tank (located under the engine)then a hose from the rear of the aux tank to the inlet for the engine cooling jacket,round the engine and out (where the thurmostat is usualy located)back into the Rad.
I doubt if I have an air lock 'cos with the rad cap off Ican see the water whizzing round nicely

(and with an air lock I doubt I would be able to get 6and a half ltrs into the system)
I am at present using the original rad fan which is way too fat

and preventing me from getting enough room twix rad and mudguard without fan fouling the spark plugs,and the M/guard fouling the rad when braking(How did you overcome this?)
I hav'nt a W/Shop manual for the Commander so I used the carb settings for the Classic,I have more or less got them sorted(with some tips from Paul)
untill I have the overheating sorted so's I can give the bike a long motorway blast to fine tune them using the exhaust colour as a guide.
I am thinking of fitting two smaller low profile fans."A"to assist with the cooling and "B"more room twix rad and mudguard.
Any tips/advice will be most welcome. and photo's will have to come via a friend if I can find one willing enough.J.B.