I've changed transmissions in my truck and now I cannot get the thing to start

First off automatic transmissions have neutral safety switch that prevents it from starting in any gear besides park or neutral. I can’t say for certain if the 1990’s had a first gen 4L60e or not but if so the gear selector is tied in to the neutral safety switch at the transmission by 2 separate harness connectors that send the gear position back to the pcm. If the neutral safety switch is not synced or positioned right then it will not send the proper signal back to the pcm for starting or shifting purposes. You may need to change or replace that component to accommodate for a manual transmission.