I recognise your dilemma from my own past experiences, you are becoming overwhelmed by your own success in identifying and centralizing your own code but lack a prolonged disciplined way of identifying things. As the months/years pass you slowly develop different naming conventions, and start investigating different methods then when you look back you cannot quite remember what does what.
I bet you lose a lot of time trying to find stuff you know you’ve written, but have to look at old code to see what the dependent file is called and its function signature.
Taking some of your points out of order:
So for something dealing with the inventory it might have an include file that includes 10 or so functions that relate to the inventory system.
If they are so related then it might be time to look to using OOP techniques.
So I was thinking about storing each function I’ve written in it’s own file, like “function_adjust_item_inventory_count.php” and then including only the necessary functions required into one main include for that specific page request.
Another reason to use OOP and then PHPs autoload feature.
This is where the naming of things becomes critical, and taking the time to study OOP properly and with it the associated “enterprisey” disciplines will (eventually) make make you a better programmer because it will expose you to predictable guidelines e.g classes are described with nouns, their methods with verbs.
Given your comments here is a trivial example of what I mean let say your inventory is of T shirts, and you operate an online shop.
<?php
// autoload will go and find the file containing this sole class
// if you have set everything up correctly, include directories etc
// this file will be auto discovered var/www/includes/classes/tshirtshop.php
$tees = new TshirtShop;
// TshirtShop is "A tee shirt shop", a noun
$tees->updateInventory(23);
// I am telling you "A tee shirt shop" to go away and "update inventory",
// not update a price, not update a colour ... update, a verb.
Your question seems to me to be more about making yourself more productive and OOP would seem to offer the structure and benefits you are seeking - I have only highlighted a couple of benefits - those which address your specific points.
Have you looked at using OOP previously?
My biggest fear is that this might add noticeable delay in the page render times.
If your app is not slow, I would not worry about it, either prove it or disprove it. Add more RAM or add a memcache like APC first. If you are a metal hugger and really want to peer into the guts of what is going on install XDebug on your dev server and go through your cachegrind files – that’ll tell you what PHP is up to, but its likely to be nothing compared to the amount of time you spend connecting and moving data from your database.
The slow query file on your database will likely throw up the most likely candidates, or maybe you have old nested queries that could benefit from some Joins instead.