I like the idea of this class, but I feel like it's a bit over-engineered for 2e. I have some ideas that I think would help in terms of simplicity and balance, which you might consider:
* Break the whole system down to specific runes (or words of power), where each rune of an incantation normally takes one action. They would break down to two categories: effect runes and metamagic runes. For the sake of balance and cohesiveness, there should probably be a limit of one incantation per turn, barring specific feats. But the result would be things like casting Fire + Widen + Empower with all three actions for an approximation of Fireball (I'm imagining the default reach would be maybe 15 or 20 ft) , or casting Shield + Stun for a rough equivalent to 1e's stunning shield (the Shield rune would specify that additional effect runes apply to the first creature to hit the target). This would reduce the metamagic rules and effect tables to one table of runes. You could also give each rune a level, and make the arcana check based on the total level.
* Instead of an additional arcane check for every single spell, maybe have penalties for casting two- and three-rune incantations, kind of similar to the oracle's curses. The two-rune penalty would be relatively small like making you stupefied 1 for one round. The three-rune penalty could be something like stupefied 5 for multiple rounds, and you can only cast a one-rune incantation next turn at most.
* Base effects off cantrips as much as possible, since this is in a way a cantrip-focused caster. For example, the base damage of the Fire effect probably shouldn't go much higher than 1d4 per half level like Produce Flame. Higher-level effects should require disproportionately higher effort.
* For balance and flavor, maybe have Incanters learn runes/words of power similarly to Wizards. Though instead they deconstruct spells, for example learning a selection of the runes Fire, Reach, Widen, and Empower from a Scroll of Fireball.