My 2000 S has also had the newer MAF & software installed and the idle does jump a little bit. It isn't major but you can watch the needle move 1-200 rpms when it used to move maybe 50-100. My battery was disconnected as well.
Yes l8braker otherthen the idle it was running in top shape.
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-99' Zenith Blue 5-spd...didn't agree with a center divider on the freeway
-01' S Orient Red Metallic 6-spd...money pit...sold to buy a house