So after much discussion with people @Jamie V who are way smarter than me with tuning and quite simply have more time/experience in this actual scenario I've come closer to fixing my issues. I hope I get all the steps correct down below so others can benefit. Stalling issue going into gear was more of a timing control issue and took some steps to fine tune, but I have it about 90% working now. The harsh shifting into 4th issue was simply having the converter locked up during shifts. I've changed it to only lock in 4th gear now, and also delayed the lockup 3 seconds. Still playing with line pressures just a bit, but it's comfortable during normal driving situations now.
So these are the steps it took for me to get the going into gear issue solved, which somewhat follow with Stinger's suggestions getting IAC position to be around 15-20%... just take it extra steps to "catch" the idle speed better/quicker using timing control and idle VE as they function much quicker than the IAC does. These steps will take a lot time and lots of gear changes! You could also use these steps for anything that puts load on the engine at idle... A/C, power steering, clutch release, etc.
1. Warmup engine to operating temps. Helps if transmission fluid is hot as well. You want everything at operating temperatures.
2. Unplug the IAC.
3. Disable ALL spark advance tables. (MAT-Based Timing Retard, Idle Advance Settings, Idle Timing Correction Curve) You want to know the timing you're commanding in the next step is accurate. Make sure to take notes of these tables so you can fill them back in later.
4. Adjust the throttle blade screw to target idle speed. In my case this was 750rpm. This step could take some time to get as close ads possible. MAKE SURE TO CALIBRATE TPS AFTER THIS STEP!!!
5. Go to the Ignition Table and adjust the fields where the "floating bubble" is hovering over. (Example: Fields are 17.1-17.6, change them all to 17.)
6. Raise the timing value in those fields by 1 degree increments and watch RPM and MAP. You're looking for the RPM and MAP to raise at a certain timing value, for example 22 degrees. This is basically where your engine makes the most power at idle. Once that timing value is determined, in this case 5 degrees you can set the timing fields back to their original values.
7. This 5 degree timing value will be used to help setup your Idle Correction Curve. When the RPM drops 50, 75, 100rpms the timing needs to be raised and conversely retarded when it rises in rpm. I'm still playing with these values slightly, but you can see the general idea in the screen shot.

8. I then used Idle VE Settings to essentially do the same thing as timing using fuel. The idea here is to get the "floating bubble" to center itself as best you can in the table while running at your target AFR. Targeting a slightly richer AFR here may help as the engine will make more power with more fuel. I'm trying to target 14.5 currently at idle.

9. Plug in the IAC and adjust your Closed-Loop Idle settings and Initial Values table to further control idle speed. Basically the IAC is the last thing to control idle as it typically reacts slower. This might not be as true with PWM IAC motors, but the older Ford IAC is slow.
Hope this helps someone as it greatly helped me. These steps were given to me by a member of the Lightning community that spent 40+ hours just sitting in his driveway figuring out. It made my process vastly quicker overall! I also took a LOT of notes throughout the process and saved tunes with basically every change so I could go back if needed.
So these are the steps it took for me to get the going into gear issue solved, which somewhat follow with Stinger's suggestions getting IAC position to be around 15-20%... just take it extra steps to "catch" the idle speed better/quicker using timing control and idle VE as they function much quicker than the IAC does. These steps will take a lot time and lots of gear changes! You could also use these steps for anything that puts load on the engine at idle... A/C, power steering, clutch release, etc.
1. Warmup engine to operating temps. Helps if transmission fluid is hot as well. You want everything at operating temperatures.
2. Unplug the IAC.
3. Disable ALL spark advance tables. (MAT-Based Timing Retard, Idle Advance Settings, Idle Timing Correction Curve) You want to know the timing you're commanding in the next step is accurate. Make sure to take notes of these tables so you can fill them back in later.
4. Adjust the throttle blade screw to target idle speed. In my case this was 750rpm. This step could take some time to get as close ads possible. MAKE SURE TO CALIBRATE TPS AFTER THIS STEP!!!
5. Go to the Ignition Table and adjust the fields where the "floating bubble" is hovering over. (Example: Fields are 17.1-17.6, change them all to 17.)
6. Raise the timing value in those fields by 1 degree increments and watch RPM and MAP. You're looking for the RPM and MAP to raise at a certain timing value, for example 22 degrees. This is basically where your engine makes the most power at idle. Once that timing value is determined, in this case 5 degrees you can set the timing fields back to their original values.
7. This 5 degree timing value will be used to help setup your Idle Correction Curve. When the RPM drops 50, 75, 100rpms the timing needs to be raised and conversely retarded when it rises in rpm. I'm still playing with these values slightly, but you can see the general idea in the screen shot.

8. I then used Idle VE Settings to essentially do the same thing as timing using fuel. The idea here is to get the "floating bubble" to center itself as best you can in the table while running at your target AFR. Targeting a slightly richer AFR here may help as the engine will make more power with more fuel. I'm trying to target 14.5 currently at idle.

9. Plug in the IAC and adjust your Closed-Loop Idle settings and Initial Values table to further control idle speed. Basically the IAC is the last thing to control idle as it typically reacts slower. This might not be as true with PWM IAC motors, but the older Ford IAC is slow.
Hope this helps someone as it greatly helped me. These steps were given to me by a member of the Lightning community that spent 40+ hours just sitting in his driveway figuring out. It made my process vastly quicker overall! I also took a LOT of notes throughout the process and saved tunes with basically every change so I could go back if needed.


