Your Instant Flash problems are not my experience with my Z77 EX 4 board. I've used it exclusively for UEFI updates, and it has worked perfectly. My first Z77 EX 4 board came with UEFI version 1.20, and I used Instant Flash for every update up to 2.80, each worked perfectly the first time. Perhaps your problem was the beta UEFI version?
Your hardware monitoring problems may be due to using Fast boot. I've noticed similar issues using Ultra Fast boot with Windows 8, although they are limited to missing fan speed readings. I don't use any of the utilities you mentioned, but have seen the missing fan readings in AXTU and HWiNFO64. If I disable Fast boot completely, none of the fan readings are missing.
My theory is Fast boot skips a step in the initialization of the board's monitoring chip, which causes the missing readings. When this occurs, AXTU will show a fan speed of 0, although the fans are spinning fine. I can also change the fan speeds fine with AXTU, but they still read zero.
Regarding your fan speeds, we are using very different fans, since I can get all of mine well under 1000 RPM with AXTU. But I don't use any fans smaller than 120mm.
My board had a recent UEFI update that added a new option to the CPU fan speed options, called Custom. When set to Custom, you then enter a number (I think between 1 and 200) which allowed me to slow the fan below the usual Level 1 speed of Automatic. The Custom numbers are arbitrary, meaning you must experiment by choosing a value and then see what fan speed is the result. Numbers below 100 resulted in CPU fan speeds lower than I have ever had, at least with the fans I use.