Unplugging that connector was done to solve a real common problem on GM front-wheel-drive cars. Yours is computer-controlled and it sounds like the battery might have recently been disconnected and the computer has to relearn the characteristics of the four clutch packs. Usually that doesn't take more than a few miles and a few shift cycles, so if it doesn't clear up, having the computer reflashed may help. That involves installing new software. Your mechanic can also drive the car with a scanner connected to view what the sensors are seeing when the rough shift occurs.

That might make sense considering the car had been sitting for over a year and replacing the completely dead battery was the first thing I did. Since it's not registered yet I was only able to put 10-15 miles on it. It had done the hard shift thing 4-5 times before I became concerned and parked it. Thinking back, it did seem to get better with each time.

I will drive it around and give it more time and see if the problem gets better. Do I risk doing any major damage driving it this way? How long is too long before I should stop expecting it to clear up on it's own?

Usually this relearn doesn't take real long. Each time there's a shift, the computer sees the volume of fluid it takes to apply each clutch. Many years ago as hydraulically-controlled transmissions wore down the clutch plates, shifts became sloppy and delayed. You had a year or two of warning before the transmission needed to be rebuilt. With yours the computer starts out with factory-programmed shift schedules which is what it reverted to when you put the battery in it. At every shift the computer learns how much fluid it takes to apply each clutch and it will update those shift points as necessary to provide a crisp, solid shift that isn't too harsh.

As the plates wear down, it takes more and more fluid volume to fully apply the clutches. That's where the older transmissions got sloppy. With computer controls and high mileage, during an up-shift, the transmission will engage third gear, for example, then release second gear a little later. That overlap gives the higher clutch time to fully engage.

The disadvantage to this system is you don't have any warning that wear is taking place. One day it will shift fine and the next day there will be excessive slippage in one of the clutches. That slippage is detected by the incorrect ratio of speeds from the input speed sensor to the output speed sensor. When that is bad enough it will default to "limp mode". It will bang back to second gear and stay there until you turn the ignition switch off and restart the engine. Limp mode lets you drive slowly to a repair shop without needing a tow truck. The system will also go to limp mode when there's an electrical problem, typically due to a bad speed sensor.

As a general rule, if it starts out in second gear as soon as you shift into "drive", it is sensor or electrical-related. If it starts out in first gear like normal, then goes to limp mode during or right after an up-shift, it is likely clutch wear-related indicating the need for a rebuild.

The Electronic Automatic Transmission Controller, (EATX), will store fault codes that indicate the circuit or system that needs further diagnosis. Your mechanic can also read the "clutch volume index", (CVI). That is a set of four numbers that represent the volume of fluid it takes to apply each clutch. As the plates wear down it takes more fluid to fill in behind them. An experienced transmission mechanic can tell the approximate remaining life expectancy of the transmission from those numbers.

As long as we're on the subject of computer relearn procedures, you may have noticed the engine idle speed is too low. You may need to hold the gas pedal down 1/4" to get the engine started, it won't give you the nice idle "flare-up" to 1500 rpm at engine start-up, and it may stall at stop signs. The Engine Computer has to relearn "minimum throttle" before it will know when it has to be in control of idle speed. To meet the conditions for that relearn to take place, drive at highway speed with the engine warmed up, then coast for at least seven seconds without touching the pedals.