The IP timing is done by turning the IP, but you should get a scanner to check what it is.
Please tell us everything you know about the truck, what model type, mileage, features, modifications, where is your PMD located, how old are injectors, fuel filter, is LP operating correctly? Are there any codes? Do you know how to check codes?
When you say a 97 transplant do you know if they just meant the cooling system update?
I doubt they would have changed the computer, but just to make sure you can remove the glove box liner, 4 screws, and then let me know the part number on it, or just the 4 letter EPROM code if it has one on the top right corner of PCM sticker. You shouldnt have to pull the PCM out to see it, but you can just pull it out, it isnt bolted down, just held tight by some clips on the front of the tray, so you can pull it towards the cab interior and it will come all the way out even without unplugging the harnesses.
With the 95 PCM you would have OBD-I, and can purchase a USB to OBD/ALDL cable to plug into a computer and see the timing, TDCO, and any sensor reading in the truck. There is a free software at Engh Motors, and you can purchase the cable from them too. Engh also sells a version of the software that also allows you to set the TDCO, which youll want to do after adjusting the IP for timing.
The TDCO is usually supposed to be about -.5, but can be advance to like -2.0 (edited, put period in wrong spot, my manual says can go up to -2.02, most people advance to -1.94) if other performance mods have been made.
The IP timing should be about 3.5* at idle, but you can get more performance by increasing the IP timing, mine is up to 8*, but idles much smoother at 4.5*. Performance EPROMs for the 94-95 in the PCM will advance the IP timing through programming. Then you can advance or retard it by loosening the IP and turning it. Towards the passenger side would be retarding it. And each mm is like 2*, so just tiny changes.
Your injectors might be bad, if the "knock" is coming from around there. If they leak while off then more fuel might be getting in oil.