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.
Alternatively, have a mage Chain Lightening a character's armor and equipment...
Firstly, he stated earlier in the thread where they found someone willing to apply the template. If it made sense in their game, why question that fact? Sure, it seems a bit cheap, but they had also via RP managed to get into the "good" books of a powerful necromancer.
I'd actually personally question the motives of the NPC necromancer doing the task, myself: if it was me running the game, I'd have the necromancer possibly include several other things on the sly: 1) provide constant knowledge of the whereabouts of the character 2) enable reliable scrying on the character, 3) ability to dominate the character 4) prevent the character from being able to cause harm to anyone bearing the necromacer's arcane mark. 5) ability to cast geas upon the character 1/year.
Powerful NPCs always have hidden agendas. Giving away items that have hidden powerful abilities is a relatively easy way to achieve this.
Instead, I'd look at limiting the amount of HD the armour can command, the effective range, making them level dependant or somesuch (perhaps he has, we don't know).
Suggesting a conflict with the intelligent armour is a good idea: such is more likely to happen 1) when the armour has a goal that conflicts with the character 2) when the character is in a weakened state
Which raíses questions about the goals of the creator of said armour. The armour is obviously going to try and seek out the most powerful necomancer in the game, because then it will be able to control more undead.
About the armor, it's a series of things I let the PCs do when they didn't have enough contacts to prevent backfires; as such, I'm planning on messing the armor up at some point. At the moment, the limitation I am imposing is that the armor can give out no more than two different commands, because giving a command is a move action. And I'm only allowing it with intelligent undead (most of them by now - the guy's burned 1000 xp on awakenings already).
He asked the armor to be crafted with the exact purpose of "serving him in the most loyal of ways", and asked for the alignment to match his one (LE). He did ask a member of the shady Thieves' Guild, which was not a safe move. The "friend" necromancer who spellstitched him of course knew of this request, so I can surely say that he interceded and changed the behavior and purpose of the intelligent armor, without the party knowing. I do need for the armor to become something they take for granted though.
This powerful necromancer has his own agenda, of course, and it'll come into play at later levels.
About the spellstitched template, I don't feel it's ridiculously overpowered, applied to a spellcaster, since the SR and saving throw bonuses will hardly come into play. The SLAs aren't terribly unbalancing with that cost.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.