Mucco, it's starting to sound like you're playing a different game than your players. You "don't want to be constantly challenging my players with monsters or opponents that exploit their weaknesses". Your players, on the other hand, want to exploit every possible weakness they can find in the rules and want to constantly challenge
you with what you will allow. Neither method is badwrongfun, but until you and your party start playing with the same mindset, you'll never really find a comfortable space in the game.
It's worth noting that you're allowing many things that many DMs would flat out disallow, and probably some things that the rules don't allow, either. For starters, consider the Spellstitched template. This is a template designed for monsters, not for players. Note that it is listed in the Monster section of Complete Arcane, and has no Level Adjustment listed for players (not LA +0, just no listing). When previously discussed on the boards (
http://www.enworld.org/forum/d-d-legacy-discussion/124863-spell-stitched-template.html) it was decided it should be about a +2 or +3 LA. You gave it out for $60k. Even if that's a lot of money to the player, it's ridiculously overpowered for the cost. And where the heck did they find someone willing to apply the template, anyway?
Also previously noted was the fact that the Necromancer has a set of armor that gives orders to undead for him. As mentioned by someone else, this doesn't work. The Necro has to command the undead himself. I also have to ask - where did the player go to custom order intelligent armor? And has the item's ego had any affect on the player (as it should)? Both of these examples are probably only scratching the surface of quetionable material that the group is playing with.
You also previously mentioned that forcing the party to have multiple encounters a day is really hard. This is simply not true. For starters, there are a ton of ways to prevent your players from taking the easy route and running away after every battle. More importantly, though, is the number of ways to make them not
want to. Any mission that has even the slightest time-dependent goal should make your players question if they should push ahead or regroup. There could be an impending apocolypse. There could be another group of adventurers half a day behind them trying to get the gold. The enemies could respawn by the time they return, meaning they never make any forward progress unless they push through. Even worse, enemies could respawn with the knowledge of how their comrades died, meaning they now know the party's weaknesses.