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I'm doing the final adjustments on my car and today run out of petrol. I was sure I had petrol so after further investigations, noticed that my fuel pump is not sucking any petrol from the left hand tank (half full). I put just a tiny bit of petrol on the right hand one and the pump immediately filled the float bowls and stopped ticking. Started the car again and run out of fuel again (pump always ticking). Looked inside the tanks, the right one was empty and the left one was half full and everything seems very clean inside.

Both tanks were washed and painted before fitting. I didn't use any sealant or anything else on them rather than petrol to wash them and on the right hand tank, screws and nuts to remove some of the rust it had. The left one was only washed as it was working before being stored 20 years ago, still smelled of petrol a lot and had absolutely no rust inside. The little filter inside the LH tank looked ok (picture below), but I didn't actually test it as it is harder to test than the RH one (which I did - if it didn't work would be easily solved by drilling a hole in it through the exit hole).

I'm using the S normal routing for the pipes/hoses and have a filter right before the fuel pump, so the problem should be the filter inside the tank - which I very much doubt to be clogged - or the union hose from the tank to the tank-to-tank pipe, which again, seems fine!

Have anyone had similar experience? Any ideas? I really didn't want to remove the tank now.

Check that the 2 breathers are not blocked on the tanks.

I'd be looking at the hard-line that your pumps are picking the fuel up from.

while the tank is empty, "blow" some compressed air into the pick-up pipe (from the pump end), you might have something in there that can restrict the flow.
I've removed all sorts of things from the "hard" fuel lines like this. silicone, rubber, rust, dirt, cork etc...

If you do this with the sender and cap removed you'll be fine.