Dude, you gotta just play a different game. If you genuinely feel you need to go through every book with a fine-toothed comb to pick out everything that might possibly throw things out of whack, playing a game with this many supplements does not sound like your cup of tea.
However, if you genuinely want to play D&D, and only wish you could feel like you did when you first played it... there is the simplest (and yet hardest) solution.
Use only the first Player's Handbook.
That's it. Nothing from Dragon, nothing from Dungeon, nothing from the AV, MotP, PH2, the Power books etc. etc. The more of these things you use to expand your game, the more the possibility of cracks will form. If you honestly felt your 4.0 game was very good way back when... force yourself and your players to go back there and play it that way again.
Is that hard? Absolutely. But it's no different than any other game that has expansions... at some point, the expansions morph the game away from what it was you originally liked, but trying to get your head around not using them just seems like an anathema.
I used to play the board game Talisman. Loved it. When the first expansions of the City and the Dungeon were released, I thought "Awesome! All-new stuff to add to make the game even better!" And for a bit, it was. Then they added more expansions, with more stuff. And soon, I found I didn't like the game as much anymore. Diminishing returns I believe it's called. So what I've done now, is whenever I play Talisman... I pretty much only take out the original game... leaving the expansions out of it. It's damn hard, cause I keep thinking "Man, I wish I could play the Chaos Warrior!"... but I also realize that Chaos Warrior was one of the facets that eventually made the game unwieldy.
And it's the same thing across the board. The World of Warcraft developers have to keep tweaking every single class, every few months... because there is just no way to keep 10 classes each with 3 specs, each with solo-play, PvE 5/10/25 man, PvP battleground, & PvP arena formatting all balanced off of each other. It's not possible. They are "updating their errata" (to use an rpg term) every single day to every single class... because there is just too much in the game to be able to balance right out. And heck... they put a lot of their patch changes into a full on open beta-test on their Public Test Realms for players to try and break... and then after months of thousands of players beta-testing the changes, they finally release the new patch to the entire public... AND STILL often have to then release another patch that fixes problems immediately discovered in the patch they just playtested for a couple months.
That's what having an expansive game gives you.
And if needing to keep tweaking things in your D&D after book after book after book gets released... you either have to live with that idea, forsake the new books altogether, or play a different game that has not expanded beyond its original (and most likely, most balanced) rulebook. It's up to you. But there's no sense howling at the moon that expansion is causing problems, because I've yet to see a game that this didn't occur.