Don't fear mods too much.
The beater I just picked up is a 95 Civic DX hatch w/ a 98k mile d16z6 swap (Civic EX motor) as well as suspension and brake mods.
Granted, I knew its history (it was a friend's aborted track car project), but it's solid. It's hard to screw up a Honda. The only things that kill 'em are lack of oil/fluid changes and overheating. Otherwise, they run forever.
Bolt-ons aren't really mods. They don't affect longevity at all.
As for emissions, RI has VERY strict emissions laws, but they don't do a visual (underhood) inspection like they do in Cali.
My car needed a new 02 sensor and PCV valve to pass, (I also did Bosch Iridium plugs and "Guaranteed to Pass" fuel system cleaner, for good measure). It passed w/ flying colors after that.
Generally, a basic tune-up will help your car's sniffer results BIGTIME.
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