Unfortunately having to remove the motherboard to get the bracket on is not unusual, they always seem to be either too small or in the wrong location.
I'm surprised it will boot without a fan connected to the CPU fan header. Most won't make it through POST if it can't sense a fan is present for the CPU. The BIOS will usually stop with a 'no cpu fan' type message.
I don't think you'll have any problem with the H50. I've built 11 systems using the H100 (120x240 radiator) and all are working perfectly with no leaks. They are very nice self contained liquid CPU coolers. I can't speak to the H50 as I've never tried one but I consider the H100 good up to about 130 watts with the stock fans. Add two "pull" fans for a total of four and it's good for over 170 watts. Provided you have good air flow through the case to keep internal temps down. Trying to cool with hot air doesn't work well whether you're blowing it over a heatsink or through a radiator.
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