What else did I forget ?
If a Generation 1, I'd consider a Tee Mod to the air breather hose a must, if you ford water deeper than 10"; Generation 2, optional.
If a Generation 1, replacement high-strength subframe bolts (or great big drill-through bolt); maybe not necessary on Generation 2s.
Replace carburetor JIS-head machine screws with Allen-head (hex socket) bolts on all carburetors (Eagle Mike has a kit). Why? After Galvanic corrosion adhesion from dissimilar metals, you'll wish you had!
Given your attention to preparation, replacement of ALL fasteners on the bike with Allen-head (hex socket) bolts appears sound maintenance. Make sure the master cylinder reservoir cover bolts are counter-sunk Allen-head (hex socket) design. At least one vendor offers an assortment with all the Allen-Head (hex socket) bolts you need for a KLR650.
Certainly, you want a hex socket metal oil fill nozzle cap, replacing the OEM plastic one.
Aftermarket air cleaner? Manufacturer? Foam or paper? Sock or not?
Custom suspension upgrades/modifications remain rather endless; e.g., what fork oil viscosity and manufacturer will you use? How much? What rear shock setting? Replacement? Stock front fork springs?
Road pegs with your crash bars? Reinforced foot peg mounts?
You may be attracted to the, "PCV Valve Mod," for the advantages claimed by its advocates (full disclosure, I am not).
The MC Mod delivers substantial "Free" increased power, according to its advocates (I remain skeptical).
Safety-wired oil drain plug and oil filter consideration on another thread.
Here's hoping you find the KLR650 meeting all your criteria; hope you share your modifying/farkleing adventures on this website, with pictures.