This is an interesting concept. I'm going to sort of random-walk through questions/concerns/comments.

First of all, with regards to the casting system, can you prepare a spell in multiple levels, and therefore have it accessible on multiple recharge counters? Like, if I was 9th level and prepared Empowered Fireball in a 5th level slot and regular Fireball in a 3rd level slot, could I cast it two rounds in a row? This feels like it might not be necessarily unbalanced, but could be against the themes you're trying to use with the class.

Second, the mechanic is especially powerful when it comes to spells that have durations of 1 min/level or longer: these spells can essentially always be kept on with minimal effort, even multiple instances of them at once! Also, utility spells like, for example, teleport, can be used on a pretty short timer. This isn't necessarily broken with a fixed list, but it makes for some interesting abilities.

Tunneling Spell might do better to be a little more standardized and just target Touch AC. As is the interaction with Monks is pretty weird, and there are probably more weird interactions as well; this is what Touch AC is for. As for if the cover breaking effect is broken or not, I'll say it's very strong when used in an unfair way set up in advance. Limiting the use on a long recharge timer might do better for it than a big per day allocation that can be burnt all at once to magnify that unfairness.

Spell List Comments: It looks like you kept yourself to SRD and Spell Compendium.

Zeroes: Repeatable Detect Magic is very good. Offensive options here are fine too.

Firsts: Some really good spells here for the mechanic, in particular Detect Secret Doors. A very strong selection of different combat spells too.

Seconds: Resist Energy is probably broken here, as you can cover the whole party with every energy type for a long period. Maybe there should be a restriction that only one instance of each spell you prepared can be active at once?

Thirds: Arcane Sight is a luxury almost no other caster can afford to use practically, but a fun one. Dispel Magic is extremely strong with this mechanic, and nondetection is as well. I was surprised not to see Hailstones on the list, it's a staple SC spell and a near clone of Scorching Ray, which is with the 2nd levels.

Fourths: Arcane Eye and it's successors are another case of "really strong" using the repeatable spells. Scrying too. The supply of good attack spells really dropped off (though Solid Fog is good), this is a class that appreciates Metamagic a ton. Lack of Orb spells is probably fair.

Fifths: Repeatable Wall of Stone is definitely itself.

Sixths: Wall of iron weirdly is less impressive than Wall of Stone, considering the circumstances. Not much else to say about stuff here.

Sevenths: Greater versions of a lot of previous good interactions.

Eighths: Repeatable Mind Blank and Discern Location is super ridiculous.

Ninths: Foresighting the party is fun but not that much better than Foresight on yourself. A pretty reasonable level.

The teleport enabling class features are a bit weird in the context of the repeatable teleportation spells already on the spell list.

Overall this class is very strong. I would probably call it Tier 1 even with the limited list, so many of the spammable interactions you can't really get anywhere else and they do a wide variety of strong things.