Save yourself a lot of grief and slow down and try to get your head wrapped around this. It took me a long time to get the script delay issues under control. It was extremely frustrating and I almost quit modding Skyrim because of it. However if you understand the issue and put in some extra work you can make it tolerably manageable.
When I first started modding Skyrim years ago my combat scripts would take 2 or 3 seconds to complete. My mod has features no one else has (or even want to try to do) because I am creating a combat simulator (I am a real life melee weapons practitioner for 30 years with our organization's highest rankings...er at my peek anyway
) and basically completely overhauling the vanilla combat system.
After 3 years of massaging the scripts and using every trick possible to “speed up” the execution I have gotten the script “speed” down to 0.2 to 0.3 seconds (at worst on rare occasions 0.5). That is still horrible for combat modding (were combat events occur in 18 to 20 milliseconds) but the way I apply them in my mod it is “acceptable”.
For example damage done to an actor is a drain effect and not instantaneous. But then that is actually more realistic for combat simulation anyway. So it is “acceptable”.
If you are not already aware SmkViper is the VIP programmer that created this scripting system for Bethesda. So it would be in your best interest to not brush off what he is telling you so quickly.
That said, I have in fact used higher than normal settings for my [Papyrus] INI settings for the last several years and I have never had any issues. But I also do not load hundreds of mods nor use mods that devour the frame rate such as HD graphics mods.
The first thing you need to understand is that the scripting speed is directly connected to the frame rate. Some functions only cycle once per frame! So for example if you use a while loop with such a function you could easily delay your script several seconds.
So the very first thing I suggest you do is remove any graphics mods (or any mods) that effect frame rate that you can live without. Then look at your scripts for any looping functions or functions that go thru long lists until done or are repeated over and over.
Move any thing you want done quickly to the top of your script and things that are ok to be delayed to the bottom. Functions at the top of the script run FIRST and so can get done faster than those at the bottom especially in very long scripts. For example all my calculations for my notifications (such as converting large float variables x.xxxxxxxxxxxxxxxxxxxxxx to a familiar %x.xx format) and any record keeping for later is done LAST in my scripts.
NOW (finally) you raise your INI settings is small bumps until you get to an acceptable speed with the smallest change.
Edit: oh and be sure to condition the scripts so they only run when absolutely necessary! My combat scripts do not run unless the actors are in combat and around the player for example. I think you may already know that from your description but I felt I should include this anyway. There are many more tricks like this but they get complicated. The above should do the job for you!
Edit 2: actually I really wish all other non combat modders would do the same and stop their scripts during combat....