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Any advice appreciated! While riding I started loosing one cylinder. Problem gradually became worse and finally I am only running on one cylinder. If I leave the bike for a while and then start it again it partially works for while.

If it's really no spark on one cylinder and not something else (like a clogged tank breather) try to swap the coils and ignition wires. If the other cylinder doesn't run you've found the problem. Of course also check the spark plugs or replace them.

If it was a breather issue wouldn’t it happen all the time? I get the problem only when hot.
I replaced the spark plugs with new but nothing changed.

As suggested try to swap coils and ignition wires as well.
A vacuum problem builds up after a bit of riding. Usually it let's the engine stall completely after a while. Opening the tank cap when the problem occurs will make the engine run normal again.

Tried the vacuum issue solution. No change. The issue appeared once when the engine had just started.
I managed to return home with 100kph and 3.5k rpm max. Problem was limited to minimum.
I will start looking into the issue.
Measured the alternator. It gives 13.6 volts at 4k rpm with the lights on.
Measured coil resistance, yesterday.
Both give the exact same values.
Tonight I will start measuring cable continuity according to the wiring diagram.
I don't know if I have to check the power modules somehow and maybe the injectors?

Spark plugs came out with bottom one to be black and wet and top one to be white and overheated.

Any suggestions on where else to look are more than welcome!
Thanks.

Your battery voltage is a bit low, it should be more like 14.0V - 14.2V with the engine running above 2K but I doubt if that's the cause of the problem, although you should check the voltage you are getting at the coils with the ignition on. They are fed directly from the battery via the fuel pump relay.
There can be a substantial voltage drop across the ignition switch and there is a mod documented in the FAQ to fix this but it shouldn't affect the voltage to the coils, etc if the relay is good.

If you are happy with the supply voltage, first fit new plugs or at least swap them between cylinders. If that solves the issue or it moves to the other cylinder then the plugs are the problem.
If no result with that swap the coils over. If the problem swaps to the other cylinder then you have a faulty coil.
If still no change then swap the ignition amplifiers and if still no change then that only leaves a faulty ECU.

Well not quite; my son had a similar issue with his 916 Strada a couple of years ago. It started fine cold but after a couple of miles would go onto one cylinder. We used the coils and ignition amplifiers off my 907 to try to track down the problem and it ended up looking like the ECU but turned out to be pinched wire in the loom feeding the vertical coil. Replacing the section of wire fixed the problem.

Thanks. I'll follow this order and give you an update.

Things are starting to look different in respect to the source of the problem.
I replaced the spark plugs and swapped coils.
I didn't get single cylinder operation (maybe I didn't ride it enough) but I noticed the same thing as before when I removed the spark plugs for inspection.
Top cylinder spark plug is white and too lean and bottom is black and wet.
I am starting to think that the reason the bottom cylinder stops working is due to fouled spark plug.

Tonight I removed the injectors to send them for inspection and cleaning.
I also removed the fuel filter precautionary to replace it from inside the tank only to find out the anti-vapor valve to be disconnected. I don't know if this could be the source of the problem though.

Today I sent the injectors for inspection and cleaning.
The workshop informed me that they were not at their best shape. I also removed the fuel filter only to find that it was COMPLETELY blocked! I really don’t know how fuel was passing through it.
I don't know if all those could be the source of the problem but they are definitely issues that needed to be solved.
I also got a compression test gauge just in case...

Ah well! I'm sure that's a big feature of the problem. It's so easy to assume that the sparks or lack of them is the trouble.

I just finished reinstalling the injectors and replaced the fuel filter.
Took it for a ride on a big avenue with the engine on high loads and it seems ti be fine now!

Compression test with warm engine and throttle fully open showed 145psi on both cylinders.

Ok... some time ago my dad bought me a "just serviced in excellent condition" SS750S (the poor's man one) sold to him by an acquaintance who had a nice garage and "he knew VERY well his way around engines since he was a professional"

Anyway 3 months later I manage to find the time to collect the bike from the garage and on my way home it starts to splutter over 4K and ultimately one of the cilinders dies a mile from home.

I was quite annoyed and I blamed the well known Ducati reliability; my dad Is aware i know my way around the V2s , but of course "you are not a professional, you know nothing...they guy said that splutters if the fuel is low in the tank...."

So , just to give him credit, I add 10liters and it gets worse...

I did not have time so I left the bike in the garage for 3 months , in the meantime I studied all the Injection system , the wiring, I get on ebay very very cheaply a full kit (coils, a TPS , Oil T sensor, ECU, Injectors, Leads, plugs and few other bits and pieces so that when I get the time I have all I need to fix the little 750.

I finally find the time and as soon as I look in the tank I immediatly see something I dont like.... I start taking out the fuel and I I find.... shit, literally...

Pump, fuel sender, all was clogged. the vent hoses from the fuel cap to the tank were missing and the connections inside bloked by rust and muck, I am not sure how the fuel did not go out (it if did it would have been a very nice big ball of fire...) inside the tank all hoses were bloated and the pump mesh filter was full of muck.

I disassembled & cleaned everything, 2 hours later it started perfectly...

I am still at a loss, how is possible the thing could run with all that water and mud... plus, the injectors are in series.. why was it running with one only? I dont get it.

Now the bike is fine, I hade to refurbish the tank and I might need a new TPS, or just some tuning (has a small flat spot at 1/3 of throttle at 3500RPMs)

Thank got it was fully bloody serviced...

This little story just to underline the fact that often we dismiss the simple things...

Here are pictures of the tank and the muck I too off, the bottle was a 1.5L just to give the idea of the shit that was inside

I had the same thoughts when the problem occured. Wiring, coils, power units. A series of thoughts and the expectation of long troubleshooting.
Apparently the filter had not been replaced when I took the bike to an authorised Ducati workshop (first and last time) and asked them to check and replace everything as the bike was sitting for some years.