The FPR is showing normal pressure, same as before. I am uncertain about my fuel trims since I have not looked at my tune. I will check on that today and see if there's anything different.

 

Well well, the problem is fixed!!! Looks like it was the tune after all...
What happen was I am using race turner/ accessport port and who ever wrote those instructions got the injector scaler backwards. Originally, from what the it says, I was suppose to input a single value to scale the injectors. The smaller the value, the smaller the injector, vice versa. So since I had to scale the 1000cc that I have down to about 700cc, I enter in the value of 38 (which was even 2 higher than the value that they equation says: 36). Re-doing the math, I realized that they had backwards. I change the value to 52 and bam, I'm back to where everything should be. My guess on why it didn't affect me as much the first tank was that I still had some 91 left in the tank and this tank was probably the very first E85 tank that I have.
So thanks for everyone's help and thanks Cobb for almost blowing my car up for giving out incorrect instructions.

 

I was going to suggest the AP scaling but I thought they would have fixed that by now.

I had that same issue back when I was beta testing the ProTuner. It's a pita, not sure why they do it so differently.

 

Me too, I think they did the scaling and the layout differently to make it stand out from ECUflash or to be different? I don't know but they have very little support on the AP and for the amount of money that one paid for it, that's kinda BS. Mine came with the car when I bought it but if I was just some random guy off the street, AP would not be a choice of tuning instrument I would use. IMO.

Anyways, I'm glad that I figure it out and now just gotta fine tune everything again.