2nd gen Tacoma engine swap. Engine from an auto 2.7 put into a manual 2.7

I am new to the forum and Hoping someone can help me out.
I have 2005 Toyota Tacoma 2.7L 4X4 manual 5spd access cab. I put 200,000 on the truck and the motor blew head gasket. Anyway I had a friend of a friend do a motor swap for me and he got me a nice motor with 50,000 miles. It runs good I just got it back today and trying to understand a few things.
The engine that he put in it is from the a 2006 same motor, the difference tho is the engine was from an automatic. Like I said I just got it back but the idle was a little jumpy but seems to be smoothing out, also it seems when I'm in say 2nd gear or 3rd I'll be accelerating and it feels like I let off the gas just a little bit.
My question is, do you know of anything that would make an original auto engine act up in a manual truck with my manual ecm. Should I ask if he replaced the throttle body?
Sorry for my lack of Grammer and confusing post. It is my first post and I'm having trouble putting my question into words.