Hello Eugene,
By PHP settings, I meant as initial settings are different for Apache and IIS, so asked if you've set your PHP as per IIS, main ones are
cgi.force_redirect=0
cgi.fix_pathinfo=1
fastcgi.impersonate=1
fastcgi.logging=0
max_execution_time=300
You've already told about PHP limit increased to 2GB with that not working either, additionally, there is php's setting (max_input_vars), by default it's disabled with value given 1000, and most of the scripts works perfectly on these values, if it's disabled at your end, try enabling and giving value of 2000.
Also, the 64-bit version PHP that you've upgraded is 5.x, where though there are 64-bit versions available, but they are experimental for Windows environment for there is limitation in C++ compiler where long is still 32-bit, but in case of PHP 7, 64-bit version is not experimental anymore, so probably VC++ 2015 that is required to run PHP 7 have that limit removed.
You mentioned in middle of semester, so jumping to PHP 7 at this point wont be a feasible decision, but can you backup course in parts, fire up another Moodle test instance with PHP 7, restore that course and see if that works.