Wont Shift Into 4th Gear

Hello!! :) My name is Kristen. Hubby just got me a 2004 Chevy Aveo base which had a bad engine so we got the engine replaced and it wouldn't start so we replaced the starter and finally it was running but would not stay running so we replaced the alternator and finally it stayed running. We drove it but it won't shift into 4th gear. The Check Engine light was flashing so what we did was use the Electronic Diagnostic tool to check what code the engine was throwing, then looked at the code and then cleared it (while driving into the 4th gear area) and finally it shifted into 4th gear!! But if we do not use the diagnostic tool to clear the code, it would not shift into 4th gear. It got me thinking that it has to be a sensor faulty issue. Can you guys help me resolve this? I tried calling the dealer but they tried to make us bring the car in and to pay them to take a look at the car. My husband is a mechanic and is able to figure out most issues but this one got him stumped. MANY Thanks In Advance!

The Codes Being Thrown Is:
P0700 - Trans Control Sys Malfunction
P0300 - Random/multiple Cylinder Misfire Detected
P1781 - manufacturer Contrl Transmission