Vac system isn't perfect in the sense that it still holds vacuum for days but I found one hose that was visibly older and cracked and changed it. Now at least the pods still come up after I stopped the engine for a few minutes which is already an improvement.

OK that's good and hopefully removes any source of mixture weakening from air that has not past through the carburettor.
This didn't help the engine from stalling after driving for a while and I didn't dare to mess with the valve clearance yet since I don't have the tool mentioned in the manual.
For now I dialled in the idle screw on the carb as per the instructions in the manual so it idles around 950 on a warm engine. One thing I do notice now is that it sometimes idles at 1000-1100 and doesn't go down for a while...
Was the rpm measured on the car rev counter or did you have a more accurate one connected? The one in the car is notorious for being inaccurate and slow, so you cannot use it to set an accurate idle rpm.
Does the engine still have the original Weber 36 DCNVA fitted? For an engine being slow to return to the set idle rpm, that often occurs owing to the throttle plate(s) not returning to the same position every time, and that is possibly due to slight wear in the spindles and mountings - it happens with many old engines. You can even get a little air drawn in past the spindles. Check for wear there.
Also if the float bowl fuel level is slightly high, a tiny bit of fuel can dribble across into the manifold and combines with the air to hold the revs from dropping to the set idle until it is used up.
... while I search for someone who has time and will to teach me in person how to set the valve clearance and properly check and configure the carb.
I doubt you would get that tool 0016928200 mentioned in the manual for setting the valve clearances, today! However you don't need it, all you really need is a set of feeler gauges, a small spanner to fit the adjuster and another to fit the locknut. Plus the knowledge of how to adjust the valve clearances.
As for 'configuring the carburettor' - you can't configure it. The Weber (or the Solex on the 2.2) are fixed jet type carburettors and once the jetting has been decided originally by the manufacturer, it stays like that unless someone starts fitting other jets! The only adjustments you have are the idle stop screw, to set the idle revs, and a mixture screw which is badly termed in fact. It does not alter the mixture of fuel and air, but simply allows more or less of the aerated idle mixture already set by the idle fuel and air jets.
So if the Weber is the original standard one fitted to the 1.6 engine, you simply set the idle, and then adjust the 'mixture' screw to give the highest rpm and then reset the idle screw again to bring the engine back to the correct idle. What you are doing with the idle mixture screw is matching the amount of aerated fuel to the amount of air being drawn past the almost closed throttle plate(s). (Only 1 throttle plate for the progressive twin venturi carbs. in either Murena 1.6 or 2.2, as the second venturi should be completely closed at idle; but there can be two or more throttle plates if the carbs. are simultaneous opening twins such as the twin side-draught Solex on the Murena 'S'.)
Roy