D16Y5 Civic HX ECU Auto to Manual help

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It was the jumper harness, I cut one of the wires and it works now.
Just wondering what ecu are you using? I have a 2000 hx with a d16y5 and I got the p28 ecu with the obd2b to obd1 ecu jumper and I’m not sure what else I need to do in order for it to work. The car was an a/t but I’m changing it to manual so wouldn’t I have to do something for the clutch switch in order for it to start? Or is this harness not going to work because it was for an a/t???
Ok so yea I’m trying to power my stock HX with a p28. My stock HX civic comes with the motor d16y5 and an automatic transmission. I want to convert it to manual and I was told to run the p28 ecu. I guess my question is, will the stock cabin harness work with m/t p28 ecu? Do I have to run any wires for the clutch signal in order for the starter to start? Is there any additional wires I need to run or re-pin? So far I got the p28 ecu and I also got a jumper harness that will hook up to my stock harness and will hook up to the p28 ecu (obd2b to obd1 ecu).
*Splitting this topic off into it's own thread for you...*

The p28 will not work correctly on the hx's d16y5. I'm sorry you were mis-led and bought all that stuff that probably won't work as you are expecting it to do.

vtec-e is not the same as vtec. The hx lobe switching is an entirely different process from a standard vtec pattern. The D16y5 cam has 5 lobes where as the d16z6 and d16y8 have only 4.
There's a mid range power gap that be very apparent if those secondary lobes are not opened up and pretty much only the hx ecu has that functionality to do so.

Additionally, the p28 will not support the wide-band o2 sensor your car has. you'll need to re-wire that to run as a 4-wire instead of 5 wire.

So, you likely want to retain the hx computer with the hx motor. There are obd2b variants of it in manual form. I'm not sure if there is an immobilizer in there or not, but it not, it is likely your best option.

At this point, i would suggest just doing a full d16y8 changeover with the auto-manual change in play as well. These are cheap, under 500 bucks these days and you can use the p28/harness that you have already to run it with a few minor wiring changes. The rest of it will likely plug right in.
Otherwise, you're going to spend a couple hundred bucks trying to make what you have work and still be slower. the cost/benefit just isn't there, plus you can sell the hx motor for 100 bucks or something (not in high demand)
Dang ok sounds good thanks for all that info I really appreciate it. I’ll most likely just get rid of this entire project now. I’ve put too much time effort and money into it and now to find out once again that I’m going in the wrong direction I don’t wanna go back and pretty much start all over again.
yeah, you're probably best off selling the car and getting a manual one to start with. It will probably net you 0 in cost (sell for 2500 ish / buy for 2500 ish).
You can probably just score a nice EX coupe in the price and have the manual and y8 already.