Trans issues

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Hi, guys. I haven't posted in awhile because I haven't had a rolling 8g in a while. So, my ex wife wrecked my g about 5 years ago and since I had a yard I vowed to get another body to swap my motor and parts over which i did back in March. Got everything buttoned up; charged the battery, topped off all the fluids( which I thought) and tried to take her around the neighborhood.
Once I got out of my driveway she seemed to surge( idle dropping/raising) after driving less than a mile I turned around a brought it back to my house trying to figure out the issue which I never did. Finally, realized that I had one of the egr lines pinched and fixed that. But once I got the car home I realized that the tranny was low on fluid so I topped it off. Once I did that , I ran it through the gears with the e brake on. After about 5 or 10 minutes of letting the new fluid circulate I tried to take off by putting the car in D annnnnnnd... she went in reverse.
No big deal, I thought. My shift cable/linkage must need to be adjusted...and so I did that. But to this day, the car will only go into reverse ( that's in R and N). In drive it does nothing. What's funny is I unplugged the gray harness from the tranny just for shits and giggles and it recognized drive. Of course without input from the ecu, it wouldn't shift.
I was wondering if any of you guys had any ideas for me before I embark on the process of swapping in another trans which I have lying around. And on that note, what's the best way to remove the flywheel bolts. I have the tranny bolts loose on the blown motor that was in the shell but can't figure out how to remove them.

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Update: So I borrowed a scan tool because my cel was on. Came up with 8 codes
p0551 Power steering low voltage
p0102 Mass air flow low voltage
p0758 Shift solenoid B malfunction
p0753 Shift solenoid A malfunction
p0743 Torque Converter malfunction
p0732 Gear 2 incorrect ratio
p0768 Shift solenoid D malfunction
p0763 Shift solenoid C malfunction

Now, I noticed that when I originally pulled out the motor and trans in the fall, they both had that JY marker on them; the motor being from an 02 already and the tranny being from an 02 eclipse. Should, I bother swapping out the solenoids or just do the entire tranny. I'm not an electrical guru when it comes to cars other than putting in a basic stereo/amp combo but this really has me stumped.

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So, i finally swapped the tranny and I'm nearly having some of the same issues as in the other tranny. I was wondering if any of you fine people could give me any advice.

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