More than likely you have the block/heads from 01 but manifold/wiring from your 99, I took a Unichip out of a 98 wiring harness, it's just wired in to the loom next to your computer so as long as you can solder & follow the original wiring & re join it it should be a pretty easy job, you won't need to open the computer but have a look, basically they are charging you for doing a pretty simple job that's a bit time consuming.

__________________
Beaten up old 98 Gen 2 Liberty, 13.0, stock V3 STI running gear.
07 Transit motor home
69 VF & 70 VG Valiants needing full restoration
Yamaha Zooma 50cc rocket hopefully going with the Transit.