B747 Captain reported a FUEL X FEED 1 failure along with a difficult fuel balancing procedure and weather issues resulted in a diversion for fuel and a subsequent flight back to the original destination.

Narrative

Aircraft X originated in ZZZZ2; there were several write-ups on the airplane. The biggest one in my opinion being the broken chiller which was signed off as ops checked ok; yet the dry ice was loaded because it was definitely not ok. About 4 hours into the flight and a 22 hour duty period the food had become spoiled and inedible. Approximately 2 hours into the flight the tank to engine EICAS came up and so my First Officer completed the procedure. Abruptly following the movement of the switches we gained a FUEL X FEED 1 EICAS Message as well. We completed the QRH procedure and made a SAT Phone call to Dispatch to loop in the Duty Pilot as well as Maintenance. A conversation with them had confirmed that we had followed the procedure to the letter and that the aircraft was set up as per the manual. Approximately 2 hours after that we received the MAIN TANK 1;4 IMBLNCE Message. We ran that checklist and confirmed that there was no fuel leaks; but when it came to the portion that states (move fuel as needed) I elected to refer back to the FUEL X FEED 1 checklist that specifically gives instructions to move fuel if this occurred. After following that procedure we were able to balance the outboard tanks 1 & 4; but then we needed to balance the inboard tanks 2 & 3. It took approximately an hour to balance the outboards and another 20 minutes to balance between the inboards. We repeated this process 2 hours later. With the typical thunderstorms crossing the equator; I elected to stay in the seat an extra few hours to make sure that the relief pilot had good understanding of the sequence of the checklist to maintain our fuel situation. I felt that there was enough potential to compromise the fuel status that I didn't want to unduly place that on somebody else unless I was sure they had good understanding of it. I eventually picked my way through a majority of the weather and was able to complete a full sequence of checklist and fuel balancing to feel confident to take a quick 2 hour nap. Upon returning to the cockpit it was evident that a new challenge had presented itself. We could see by some of the reports that a thunderstorm was moving into the terminal area at our destination. Upon reaching ZZZZ1; the storm had made its way onto the field and there were reports of other carriers were going around. We were being diverted east of the field on radar vectors; soon it felt like the controllers were becoming task saturated with the number of aircraft in the vicinity. We came up with a number for BINGO Fuel of roughly 13.5 Tons; but quickly added to that because of the weather and brought it up to 15 Tons. At Around 17 Tons I decided to pull the plug because of a near miss by ATC that flew us directly 1;000 ft. above another aircraft and was late in my opinion with a traffic advisory. The cockpit was becoming very difficult to manage with many things going on. The weather did not show signs of improving quickly. ATC language barriers played a huge roll and led to confusion in the cockpit due to interruptions from their many transmissions. We were already under Fuel Reserves with thunderstorms between us and the alternate. Additionally; I was not totally sure of our fuel status as our secondary EICAS was compromised and many checklist have been inhibited. Ultimately; I made the decision to divert because there were so many factors and it would have only made things worse to stick around longer for what seemed to be inevitable. We then put our heads together to forge to our alternate ZZZZ3. We considered a couple of options quickly like ZZZZ4; but because we were self vectoring around a giant thunderstorm due to communication and language barriers. We elected to go to our primary alternate and started to plot a course to give ourselves some sort of situational awareness on the ND. We got ATIS and I reviewed an approach we thought we would get and I resumed pilot flying duties while my first officer set up the approach. When we entered the terminal airspace at the alternate; it was evident that there were a slew of aircraft that had the same idea as us. It looked like there were 4 aircraft to our left that ATC was going to try and put in front of us. We had around 11 Tons of fuel at that time. Not extremely alarming but I had it in the back of my mind that we had balanced fuel multiple times on the flight up and I wasn't 100% confident that the fuel system was 100% accurate. I elected to declare a Minimum Fuel situation to ensure priority and a safe landing. We were also well under our fuel reserves set. Due to the compromised fuel system I padded our numbers in my mind to allow for an extra half hour while reporting endurance. What was represented was approximately 1:15 of flying time and I declared the endurance at 45 minutes upon the [priority handling request]. We shut down with a little over 9 Tons on a short taxi which left about an hour's flying time doing go arounds if we were lucky. We reported landing with a little more than 30 minutes to the Controller.After fueling the Aircraft back up to 50 Tons and a several hour delay on the ground; the decision was made to plan to go back to ZZZZ5. I was instructed by Maintenance to try to move the fuel crossfeed valve for number one and try to clear the status message. The procedure worked and he was able to give me the verbiage to remote sign the aircraft off to be airworthy without maintenance present. To be honest I have never heard of this; but if my Director of Operations is willing to get on a recorded line and tell me it's an approved procedure; I was willing to go with it. We had the aircraft already set up at that time so we elected to push back and go. We incidentally never cleared any customs in [foreign country]. On the flight back to ZZZZ5 I took a nap a majority of the way; I was informed that the FUEL X FEED 1 EICAS Message came back up. So we wrote it up; along with the chiller and a light bulb on the overhead. I believe that we had a good safe outcome despite many factors working against us. In this particular case the major causes were mechanical failure as well as weather playing a strong role. ATC also created some confusion and there were so many airplanes all trying to get into one airport at the same time it made it very difficult for both them and us to fly around in a bowl.I suggest we look at that checklist FUEL X FEED 1; for specifically the #4 crossfeed valve positioning. If we left the airplane alone and let it do its tank to engine; my belief is that it would've kept even tank values. We had difficulty understanding foreign Controllers and we let them speak to us way to often and that may have been avoidable with giving them even less information and a little more direction.