How can I speed up INNODB queries comparable to MYISAM performance?

Hard to say without knowing too much about your environment, but this might be more of a database tuning problem. InnoDB can be VERY slow on budget hardware where every write forces a true flush. (This affects writes, not reads.).

Run explain for each query. That is, if the slow query is select foo from bar;, run explain select foo from bar;.

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