Yeh the N/A Gen 2 3SGE doesn't use AFM. I've tried unplugging the air temp sensor when I had a Gen 2 N/A and didn't do much no fault codes or anything. If anything might be slightly richer.
I had exactly the same issue with your hesitation after my engine swap, anything more than 1/4 throttle it would bog down. At WOT it would just stall (or very close). Very annoying lol. Problem went away after a few drives and I added fuel injection cleaner which helped I think. I'm guessing changing the fuel filter would also help if you haven't done that.

well fixed the "hesitation" ... not even thinking about it before this morning I woke and found myself saying ... "hmmm, I wonder if it's the HT leads" ..... so I pulled the new ones I recently bought, off my old engine, dropped them onto the new one .... hey presto .... works nicely. as for the Knock sensor, the mechanic had an apprentice working on my car, he broke it (the connection off clean) , and didn't tell anyone.... the air temp sensor under the lid, is basically only there for the engine bay fan (according to the electrical schematics I have read).
 
So to sum up, it is now running nicely, from the very short drive I got to take it for after fixing the last of it at work, the only bits and pieces left is this odd reverse light not working, (turns battery and oil fill lights on (in dash)) along with very lightly illuminated battery and oil fill lights... and the engine bay fan, seems to be getting stuck somehow, I am definately leaning toward a bad earth in the circuit there somewhere...
 
Thanks all for the prompt answers, has definately let me "vent" and given me a lot more ideas towards these problems I have been having. I hope I do not need to ask too many questions, and can start giving some answers instead.
 
:D
 
oh ... as for the AFM I would think he was reffering toward the throttle body and throttle position sensor.

Ahhhh.... Air Intake Temp sensor, ... hmmm would have thought he would have meant the throttle position sensor as that does basically the same thing as an AFM, but not as accurately, whereas the air intake temp sensor is totally different.... neither here nor there. I have dropped a PoD finter on mine and plumbed the vaccuum and AIT sensor both into it, runs so much  better I found, has a nice growl through the intake, but I need a bigger exhaust which will quieten it down some. Heard of a guy on the northside here in bris that does nice full sytem for these including high flow cat for $400 ... so when I recover from the trauma this recent event has done to my bank account Ill be looking into getting one made up.... and hopefully soon enough will have a full running gear / exhaust / and harness + ECU for sale .... after I buy the 2GR to replace it that is, any volunteers to help fit it when it happens?? ..... bound to be lots of fun ... promise :D
 

Yeh pod makes awesome WOT roar, screw exhaust I say lol (4 banger NA sound crap imo)
$400 not bad. Including manifold? Wait Northside? Just beware we have a member on here that had bad experience with them, just letting you know whether you decide to do it or not.
MR2 was destined for that 2GR!

^ Nothing to do with Captain Sensible and 1981?

Well AFM or air temp sensor or MAF or MAP either way they all ultimately measure air flow regardless :/ we're just being touchy technicals haha
WOT - waste of time. Cars...