According to PokeGen which is my goto for gen 4 pokemon editing there are several dozen across all methods documented at the the time of it's most recent release. (there is no way i'm typing all that into a spreadsheet :P) AFAIK method 2 and 3 are common to emulators and have basically never been confirmed on og hardware. for more info check this smogon writeup
Have you tried opening the edited save in pkhex after exporting it to check if the changes are seen by it? Did you make sure to click save in the items window?
For gen 1 and 2 you can use pikasav. For gen 3 you can use a-save by kazowar. For gen 4 and 5 you can use pokegen by codr. All of which are available in the downloads section. If you want to edit more than pokemon and items I don't think their is anything public to do so except a mystery gift injector for gen 3.
You'll be fine. Although if you change the base stats of a mon that happens to be in your party, it's current stats won't update until it levels up iirc
If you're editing a mon you need to set it back to a spot, otherwise you can try closing pkhex completely then reopening it and loading the just exported sav.
For a mon to be shiny the PID, SID and TID are run through a calculation and the result determines if the mon is shiny. if you change any of those values the mon will most likely no longer be shiny. ".PID=$shiny" makes the mon shiny (by changing the PID )based on the new TID and SID but breaks the correlation between the IV's and PID for Gen 3 and 4 mons. If you don't care about the legality of the mons (or using them online including sending them through the bank) you have no further issues to worry about.