Uhm... ok?
Ofcourse it takes time for PHP to parse functions. That's a given.
If you have one big file now, it means that each script parses a lot of functions that it doesn't really need. agreed? agreed, because that was in your original post.
Now, if you make smaller files that contain only the functions that each script needs, you end up making copies of the functions because some functions may be required in several scripts. And that's not what you want (unless you are a workaholic)
Thus you end up with many smaller files, some with functions that are special for one script, some with functions that are used in several scripts.
Then it's down to benchmarking to see which is faster,
but more importantly, can you maintain your scripts if there are 46 of them, all with different relations to eachother?