Ingector pump timing and not changing gear

Hello
I have a 1995 Chevy c1500 with a 6.5 diesel its my every day work truck it has covered just under 200,000 miles it was breathing badly and the head gaskets had blown, I have just changed the engine for a 6.5 with only 57,000 miles on it, it is running starts up good no breathing anymore but there is a bit of injector noises and it dose not change gear, I did lose some transmission flued during the engine swop, I think the injector pump needs timing, the engine I put in had no injector pump no injectors no water pump no manifolds so all that is off the old engine, any way I have some codes here they are. 13, 17, 18, 34, 36, 57, 81, 82, 83, 84, 99. I live on Anglesey North Wales UK and the nearest person I know with a tech 2 with a NAO card is 150 miles away, any help would be appreciated.
Thanks,
Duncan.

First, look at all your power and ground connections. All the PCM grounds should go to the engine, and from there to the battery. So many codes seems to indicate something didn't get reconnected properly.

Then, look at the ignition switch. Codes 81, 82, and 83 are transmission related and will occur when the power to the trans is flaky. The trans and some of the instruments (tach, for example) are powered separately by the ignition switch.

There are a few wires at the rear of the intake manifold that fasten to one of the intake bolts.

These are important grounds....be sure they are there

On LEFT HAND DRIVE RIG these wires are by the RIGHT REAR of the intake by the dipstick tube....

How did you replace the injection pump (Locating it) ????

Thanks JohnC and Robyn,
Quick up date, cleared the codes, toped up the transmission, drovit up the road and it changes gear, when I got back on tickover the service engine soon light came on, read the codes got 34, 36, 81, 82, 83, so there is stile some think going on with the gearbox but it changes gear, and 34 36 pump timing.
I replaced the pump with the one from my old engine I am pretty sure I got the pin in the right hole, the injector noise is not as bad as it was, the old engine was quiet could have been due to low compression, how much injector noise should it have it dose sound like a direct injection?
Will look at all my power and ground connections the wires at the rear of the intake manifold that fasten to one of the intake bolts tomorrow there was a ground wire that was trapped under the rocker box by the dipstick I left this on the old engine and did not put a replacement there will do that tomorrow, it was a braded wire will let you know how I get on tomorrow.

I have had to work for a few days and had to borrow my brothers truck witch is very good of him, but I want my Chevy 6.5 back, it changes gear now but the timing needs sorting, so after looking in to the timing from all angels I have tried moving the Optical Sensor in side the injector pump the engine sounds a lot better, has any one had success altering the timing this way? its the only way I can think of doing it with out a tech 2 and NAO card, the old engine was breathing and had low compression so would of been quieter than normal, going to tack the Chevy for a short run tomorrow and see how it runs.