I came around fixing the reported issue with the enabled bogomem (fake Fast Ram) setting, you can find the simple fix in the recent update:

• Fixed MOVEA.W reg,Ax - source data was not sign-extended

Now the Kickstart starts with both bogomem enabled or disabled configuration.

Some details on the fix

Debugging an emulator needs a completely different approach than debugging any other application type, simply because even if one or two instructions were misbehaving it doesn't mean that the emulated program is not working at all. It just does weird things, but not on the good way.

In this specific case when the error was: if the bogomem configuration was enabled then the Kickstart went into the dreaded reboot-loop, which is basically the result of an internal crash, usually because of a wrong access of memory somewhere or an exception while another exception is executed.

I had a closer look on what is going on and I have found that an instruction is trying to write into a custom register for the disk controller which is read-only. Never a good sign, especially if the Kickstart is trying to do that which is always playing by the (hardware) rules.
It was an even more interesting fact that the wrong-doing instruction was only for reading from memory.
My reaction was a confused face with a hint of suspicious look. I am still a bit puzzled by this, even after the fix - this must never happen ever.

But at least we have a crash!
It is always easier with a crash, it gives a starting point (or so I thought at least).

First I tried to log the full execution and analyze it for a while, but the only thing I had found was that some hardware handling loop runs too long, probably this is why the Kickstart hits the custom register by accident. This is not helping at all, usually it means that some initialization or leaving condition for the loop went wrong, so I had to look further before the loop itself.

Luckily, the Kickstart with this configuration set was working when none of the instructions were compiled. There is a simple method for finding out which instruction(s) causing trouble: turn off compiling of all instructions and add them back one by one while start the emulation with the same settings over and over again.
This sounds tedious but actually it is much easier than scrolling through megabytes of debug logs and looking for something, because it is procedural. Unfortunately, this method does not work for every possible issue, especially when the combinations of the wrong instructions are causing the problem.

At the end I had found that the MOVEA.W AX/DX,AY instruction was the one to blame and a quick look on the compiled code confirmed that the emulation was wrong: for every operation where the target is an address register the involved data must be longword sized.
In this case this simply meant that the word sized source data must be sign-extended while it gets copied into the target address register. I had done this for every other similar instruction, but I missed one case.

Now, you can probably see why there is no way I could find this bug by looking on the execution logs.

Thanks to kas1e, Thunder and MickJT for reporting bugs!