are you getting any new error codes, note the codes down then do a ecu reset which will clear the codes and then see which ones come back
if you dont clear them they will still be stored in the memory and will show up even though nothing is wrong.
also could be your afm is buggered?? did you get a new one with the new engine?? if so then swap back to the old one you had and see if it fixes the hesistation problem.
for the lights check and see if you have wired them up properly and not wrong sensor
with the reverse lights. check in the boot by pulling out the carpet and see if the connector there has come off.
hope you can fix the issues

PM  sent.

No error codes are coming through, could possibly be the AFM, I do have my old one also, I may try it, am also going to ring the guy I bought the engine from tomorrow to see if he took the intake manifold off to remove the wiring, as I bought it without harness. As for the lights, I am so not sure I was thinking maybe a fuse?... is there even a fuse for solely the reverse lights? ... this matter I am more leaning on a bad earth .... but where ...
 

im leaning towrads your afm for the hesitation specially now because you have a new afm that could be a dud, put the old one back on and see if the car drives any better

If this is a Gen 2 NA that we are talking about as you stated earlier.  

 The '90 model NA does not have an AFM, it uses MAP. (see pic)
When you say AFM, are you talking about the air intake sensor that sits in the top of the NA airbox?  (It looks just like the temp sensor mounted in the engine lid). If so, that would not have much effect anyway on the problems you are having.
 

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.

The 1990 SW20 NA has a computer controlled knock sensor that adjusts itself to the fuel you are using.  This only happens when the engine Revs beyond 5K rpm and takes about 3 or 4 times to adjust correctly.  If you have, as you say, only reved it to 4K rpm then the knock sensor has not adjusted correctly.  As Tree says problem went away after a few (probably spirited) drives  ..... ;-)
 
 

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.

Glad it's running better now, when everything gets sorted out it's very hard not to be pleased by the driving feel of this car :)
My knock sensor literally "fell off" when I had a major service on the engine, looked as tho it passed thru hellfire hehe.
This is the air temp sensor we are referring to aka "AFM" (but not AFM)
http://www.toyodiy.com/parts/p_J_1990_TOYOTA_MR2_SW20-ACMQF_8404.html?hl=89424
It's attached to the air box, you'll see wires (2 colour?) going to it. As Reddtarga pointed out it looks the same as the one stuck on the lid.
RedMR2Red it was very annoying limping the car whenever I put too much throttle because once the RPM bogs down you have to feather the pedal again until it seems to "unflood" itself. My mate couldn't take it and quickly decided who was master. After a bit of resistance from the car it finally broke (like breaking a stallion) and I've had no problems since hehe

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