Okay, so here's a few things.
1) You don't really need to "incorporate AFR's" but it is very helpful. So in the future, if you decide you want to run a different AFR in a certain load point, all you have to do is change your target AFR tables, versus trying to redo the VE map.
I also really, really recommend using VEAL, it's worth the 50 dollars. You dial in your AFR table, and let VEAL do it's magic. Give it a sanity check, and go from there. Learn how to smooth out your VE Table in 3D.
2) The throttle lean issue you're having is from lack of Accel Enrichment. Every car is slightly different in it, and it's a PITA to dial in just right. And it's even worse if you decide to change injectors cause you'll have to do it again.
http://www.diyautotune.com/tech_articles/megasquirt_acceleration_enrichment_tuning.htm
Stare at this link until it make sense. AE is based on HOW fast you hit the throttle. And it's based on your driving. I can drive my miata just fine, but when someone else drives it, it has a bit of hesitation, based solely on how they drive (I haven't had a change to really dig back into this, but people seldom get to drive my car).
Another strategy for AE, is getting on the highway, in your final gear (fifth), and do varying throttle tip in's (usually with someone else driving or logging when you're driving) to get an idea on how AE works, and what changes need to be made.
Also if your REQ_FUEL is off, you'll NEVER get it dialed in right.
My suggestion would be to BOX in your idle map (use the all 9 squares around your idle) to get it to where it needs to be. Also keep in mind of the load break points, on my base map for my miata, the break points were 900, then 1200, but my idle was set at 1000, so I could never get it to idle the right AFR's because it was interpolating between two load cells, until I boxed it in, then I had an issue with tip in throttle. I rescaled my map for 500, 1000, 1700 ETC that way I could get it to hit certain load points based on my driving habits.
You might want to see if you can find anyone using your injectors, otherwise, I would look into a different injector that people have some data on (such as RX8 460's). I'm not using an L motor (obviously since my MS is in a miata), so I don't know what injectors would fit your motor.
Oh! For your MAT Correction, leave it at 100, but you have to try to tune on days that are close in temperature. Once you get your VE dialed in, at that point you'll want to play with your MAT Correction.
Also, if you log take a look at GAIR, that's the MAT correction factor.