I vaguely recall sohc single port EJ22 is an oddball thing somewhere around 97 when they went from phase 1 to phase 2. Are the valve covers on the heads the old school ones that have "16 VALVES" imprinted on them?
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If it's an 99 ecu, it's probably not really meant for those heads, probably why performance is poor. Good and bad is ecu is fairly simple and doesn't care which block is in there. Swap in the 2000 block, it's what the 99' ecu wants over all.
Or if your state emissions doesn't care, drop in an 97-98 ecu and it might fix everything; if the current block has good compression and no mechanical issues.