p1899 in a manual xj ?

The problem as I see it is that the auto ECU is expecting to watch the output of the NSS park/neutral circuit, which is grounded when in park/neutral and open (therefore floats to 12v since it's wired to the bottom of the starter relay coil) otherwise. So the auto ECU freaks out because that pin simply isn't wired on a mantrans harness, so it's seeing nothing. I'm not sure if grounding it will fix anything, it may just freak out and think it's stuck in park/neutral if you do that. Similarly, wiring it to 12v may not help either. If you wanted to install a clutch safety switch you could probably fool it, just cut the black wire from the negative side of the coil on the starter motor relay in the PDC, insert the clutch safety switch wiring between the two cut ends, then wire pin A6 on the ECU into the side of the clutch safety switch that is directly connected to the starter motor relay coil, but that's probably going overboard. I would probably either bug the shop or see if I could buy a 96 (95 and down won't work, different ECU and harness plugs) manual 4.0 ECU and install it.
 
I would bug the shop...I know I would have a customer coming back at me if a vehicle I turned out had a problem it didn't have previously...
 
I have a 97 auto pcm as a backup to my 96 manual pcm. The main issue with the auto pcm is that it doesn't have a neutral drop-out map program like the manual pcm does when you push the clutch in at higher rpms or put it in neutral. The 97 auto pcm also produced a constant light-gen light on the left in my 96, but worked.
 
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