Caster Levels do not stack
From the CRB section on magic (caster level):
A spell’s power often depends on its caster level, which for most spellcasting characters is equal to her class level in the class she’s using to cast the spell.
Caster Level (CL) is associated with the casting ability in each spellcasting class. A multi-classed spellcaster has multiple Caster Levels. Caster Levels do not transfer from class to class nor are they additive. So, a Wiz2/Clr1 has CL2 in the wizard class and CL1 in the Cleric class, he is not a CL3 in any class and does not qualify for Craft Wondrous Item.
- The Magical Knack trait in Pathfinder provides the ability to augment CL in a limited quantity, up to the sum of a character's hit dice. A Wiz2/Clr1 with Magical Knack (Wizard) would have CL3 for wizard and CL1 for cleric, and thus qualify for Craft Wondrous Item via his wizard CL.
- There are items that could help out here: The big ticket item (about 30k gold) is the orange prism ioun stone. This increases your caster level by +1, but if you go cheap and get a flawed one it also imposes a -2 penalty on your primary casting stat. So there's some give and take, there.
- Drugs! You could always take Mumia, but I think this would probably be GM dependent as the effect is very temporary and requires ongoing use of a drug that may turn you into a ghoul...
A Note on Mystic Theurge Progression
Once you do pick up Mystic Theurge (whoo!), there is the caveat that the Caster Levels from Wizard and Cleric still do not stack, but they do stack with Mystic Theurge levels:
When a new mystic theurge level is gained, the character gains new spells per day as if he had also gained a level in any one arcane spellcasting class he belonged to before he added the prestige class and any one divine spellcasting class he belonged to previously. He does not, however, gain other benefits a character of that class would have gained. This essentially means that he adds the level of mystic theurge to the level of whatever other arcane spellcasting class and divine spellcasting class the character has, then determines spells per day, spells known, and caster level accordingly.
So, a Clr3/Wiz3/MT1 would qualify for things requiring: Caster level 4, Arcane caster level 4, and Divine caster level 4. You can add your variables, like Magical Knack or items, to this base.