Transmission shifting issues?

So about 4 weeks ago I received a wrenches light come on in my dash. I used a scan tool to see what might be the issue and it read out,

1. Shift solenoid malfunction
2. Gears 2 and 5 out of sync

So, I bought a new Shift solenoid pack, new filter and gasket, and went to work on it. Took about 3 hours but got it all back together, new solenoid, new filter, and gasket went on with no leaks. Replaced the 5 quarts of fluid that we drained to remove the pan and allowed a generous 30-minute runtime to get the new fluid nice and hot. Checked fluid and had a slight stream of fluid come out so I assumed it was full. Tested the gears 15 seconds apart each Shift and all shifted fine, and so then I took it for a gentle cruise to relearn the gear patterns. After 40 minutes of no issues, I received the same codes again but this time with check engine light as well.

Now it states:

1. Shift solenoid B malfunction.
2. Gears 2 and 5 out of sync.
3. 2nd gear doesn't Shift into 3rd until about 3,400 RPMs and it shifts from 4th to 5th with no physical feel, only way to tell is to watch the RPMs drop about 1,000 from 3,300 to 2,300.

Not sure what else to check, doesn't seem to be the Servo Bore due to the lack of symptoms it states that points to that problem. Please help.