A long story but need your advice.

Was booked to fly BRU-WAW-TLV with Lot.
Sitting at the gate in BRU, I discovered that my flight BRU-WAW is delayed by over 1:30 meaning I won't be making my connection that evening (surprised that I wasn't warned at check-in).
Realising that I still had a chance to be rebooked on a direct flight with Brussels Airlines about to depart, I franticaly started serching for a representitive of Lot which was nowhere to be found, I headed to the SN lounge, which sent me to the SN ticketing desk, which informed me that I have to go all the way back to the check-in area to find a lot or swissport (handling agent) representative (was furious, as especially if a flight is being significally delayed, there should be someone in the departure area to speak to).

Not wanting to give up I approached a gate for a LH flight attended by swissport employees and asked them for their help. The LH supervisor kindly called their ticketing desk and rebooked me on a flight with LH to MUC with a hour connection on to a AB flight to TLV. They issued me with a new boarding pass to MUC and was told that the boarding pass for the AB flight will be waiting for me at the AB gate in MUC.

Upon arriving in MUC terminal 2, the airport screens referred us to T1 for our connecting flight. Since the 1972 olympic attacks, all TLV bound flights depart from a seperate highly secured terminal which is named terminal 1F. Terminal 1F is situated far from anywhere but much closer to T2 then T1, meaning that we spent a half hour running as fast as we could all the way to T1 and then all the way back to T2 and from there on to 1F (the Lufthansa ground staff manager told us that they have raised the issue with the airport authorities many times to requested the terminal to be clearly signed or renamed).

Huffing and panting we finally arrived at the gate 20 minutes before departure, where the AB staff were waiting for us. When they learned that we have no boarding cards they shockingly denied us boarding, therfor stranding us for the night at MUC, claiming that they can't check us in less then 30 minutes prior to departure and that LH should of checked us in.

Question #1: Am I right to assume that LH is to blame here for our denied boarding as they should of us checked us in for our connecting flight?

Qurstion #2: The first flight was delayed due to weather, will I still be entitled to compensation according to EU261 for being denied boarding onto the second flight? If yes which airline is here responsible, is it Lot who was the original supposed carrier, or LH for not checking us in or AB for denying us boarding, or perhaps LX which issued the tickets?