Idle Surge + low engine temp?

[smy0003]

Idle surge how?
Your thermostat could be stuck open and causing your car not to get up to temp, that would keep your idle around 1500rpm or so.

[RS2000]

However the radiator hoses, have no coolant in them, just air.

[Steampunk]

you really need to spend an hour or so reading this forum, US Miata forums, etc. and familiarise yourself with not only MX-5's but cars in general.

Firstly, there is ALWAYS coolant in the upper radiator hose. The hose sits slightly below the level of the top of the radiator, so if there's genuinely no coolant in the hose (which you can prove by obviously removing it from the radiator), that means that your radiator is not full, hence you don't have enough coolant in the system which will lead to cavitation which then leads to overheating.

Even if you have a leak somewhere near the heater core, or anywhere, your coolant level will still be replenished by the overflow (if your radiator cap works properly), henceforth your overflow bottle will eventually empty.
If you still have a leak AND your overflow bottle remains full, then your radiator cap is not working properly and engine coolant will eventually disappear.

Second, what do you mean by

The engine temperature is my main worry as it keeps reading like 2mm shy from operating temperature.

?
IF you think that "operating temperature" is when the needle is at the 12o'clock position, then you are incorrect. The needle SHOULD be 1-2mm to the left, of centre. If it moves further to the right, the engine is getting hotter than usual/not getting cooled properly.
AFAIK many, if not all, cars' coolant temp needles sit slightly less than mid-way, not just MX-5's

What do you mean about vacuum leak? If you hear a brief sucking "shhhdd" sound for half a second after engine shut off, this is normal.