What are your plans for adapting all of the sensors to the MT ECU?
For what it's worth, I believe the 1999 HX transmission is shorter than the transmission that actually want to the D15Z7, which is in turn even shorter than the transmission that went to the CRX HF which had even less power. I expect you'll be fine.
Lean burn does not kick in during city driving, at least not generally. It happens between a certain RPM range and certain load range and you'll only really see it on the highway. The engine will drive like any other long geared D15 in the city. You may not, however, even get lean burn. It's a finicky system and if a single required sensor isn't outputting in the range it wants to see, lean burn will not engage.
You may want to reach out to Rywire or Wireworx about your harness issue, it's probably something they've dealt with before.
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