Can I put a 93 Ford ranger 2.3l in my 2006 Ford ranger 2.3l?

My truck is manual, would it matter if it's a automatic or manual transmission and would the Engines line up even if it's a 93'

Not really, because you will need the computer, and the wiring harness from the '93. Even with that, it will be a challenge. Why are you getting an OLDER engine as opposed to one from the same year?