From the looks of the berry system setup, it may be easiest to turn on switches at certain stages of growth, or even go a little more complex with assigning the berries name to a variable, and check that in the event to determine which image to display. I'll have to play with it a little more.
If you're wanting it to span across the entire game, it's actually fairly easy. Me and a few others asked about it a while back, and poccil posted a balanced level script, which he was nice enough to package into the newer versions of essentials (even though i don't think it's referenced anywhere). If I'm not mistaken, the levels of wild pokemon are defined in PokemonEncounters on two lines (I'm not sure why there's two tbh). They read level=encounter+rand(1+encounter-encounter), but you can change both of those lines to level=pbBalancedLevel($Trainer.party). That should do what you're asking. If you get an error saying the method is undefined, let me know and I'll send you the script. It shouldn't be a problem unless you have a really old version though.
How difficult would it be to have the wild Pokémon's level near the level of your team?
Example: Route 1 - Pidgey Lv 2, Your Team - Arceus Lv 98, Mewtwo Lv 95.
So with the script, it'd make the Pidgey somewhere between Lv 95-98. If you have a team of six, and they're all different levels, it'd take the highest level, and the lowest level, average them, then the wild Pokémon's levels would be that average, plus one or two higher and/or lower.
I see. Did you import the resources all at once? If you do it one at a time and test regularly, we should be able to narrow down the culprit. So you can safely add all the graphics and audio at once, since they aren't a problem, but after that try importing all the maps but no scripts, and see if the error appears then. If not, maps are safe, and import major scripts one at a time. So first the menu, then test, then all the miscellaneous scripts, then test. At some point, one of those should throw the error. And just to be 100% safe, test the kit you're transferring to again before importing anything to make sure it actually works.