Great idea to get the hang of tuning before the new motor.
The issues you have are probably related to the transients that you have to tune. These are AE, DE and PE parameters. But before you can even start worrying about that, you need to get the VE and SA tables good for constant throttle.
When I began tuning, I would not make rapid movements with the throttle and surely did not go WOT. Keep doing VE learns until corrections stop. I know they say you do not need a WB to tune, but it makes it really easier. Do lots of driving for the VE learns trying to slowly vary the MAP and RPM. You vary MAP by going up or down hills.
Once you have put the time in there, start doing some 3rd gear pulls on the highway. Start slowly and adjust the AE - TPS%. This is where I started getting the SOP feel that I needed and then pulled timing out were I was getting knocks. Reading my WB, it should be at 14 at constant throttle. When in closed loop, it you should see the NB going up and down cyclically. Then, when I slowly started to do a 4th gear pull (I have a T-56), I tuned until I saw the WB dip down a bit (AE Light On - WUD). Then I compared my AFR (Commanded by EBL) to WB in the log to determine whether I was rich or lean.
There is really a lot to it, so start slow. Unfortunately, unless you get lucky with your starting bin, it ain't gonna run good out of the box. But what fun would that be??
I am on my 70th bin or so right now and still have room for improvement. Learn, Burn, change and analyze. Repeat.
One thing that I have started doing recently is make several small changed to very few parameters and burn all of them into the EBL in different banks. Then change the active bank and log. See the differences you made. Make small changes. If you get knocks, just pull less than .5 a degree.
Can you tell I'm addicted yet?

Good luck and keep us posted.
We need more info - Auto/Manual ... things Ronny was asking...
EDIT
But before all of that, read this post and get your idle set. This should be done b4 anything else since it has an affect on all IAC parameters.
http://www.thirdgen.org/techboard/di...en-coming.html (ebl: stalls when coming to stop)