2005 4.0l SOHC 220k miles

So i've been trying to diagnose a water leak this past week and narrowed it down to the water pump and/or thermostat housing. I ordered the metal thermostat housing that was recommended on this site and was planning on replacing that today. I took off some hoses, sensors, disconnected the battery, throttle body, and air intake. I needed a tool and couldn't find a ride, so I just put everything back together and headed to the store. I noticed I have 0 acceleration and something feels "off". About 5 minutes into driving at around 50mph, my O/D light starts flashing and it starts driving rough. I'm about 90% that I put everything back on correctly. The 0 acceleration thing has been an issue the past few months just not as bad. Tranny fluid seems to be okay. I've read other threads on this and they all have a hard time shifting from 1 to 2. My truck doesn't seem to have any problems shifting. Could this just be an electrical issue? Maybe air leak?

Unrelated problem (i think): My windshield wipers have not worked for over a year. I need to replace the multi-purpose switch but have been putting it off. Could this be related somehow?

appreciate any help

 

Update: just gave it a test drive (about 25 miles) and I did notice that it is shifting pretty rough. There seems to be a "lag" in between gears