Rep Power: 0

I'm going to try to get as much info in the shortest post I possibly can.
Anyways, I have a 2005 Honda Civic LX, completely stock. Automatic transmission.
Keep in mind, the car was shifting REALLY hard into 3rd gear, already. (I know, I shouldn't have driven it after that, but I had no option)
The other day, as I was driving to work, the car went into "limp home mode". I drove it 2-or so miles more, to get it out of the road, and then had it towed home.

Now, the check engine light is on, and I don't have an OBDII reader so I had to use the trusty ol' jumper from pins 4 to 9 on the OBDII connector.
Check engine light blinked and gave me code 7 (or 07, rather).
After doing a little research on that, I decided to check and make sure I read the pattern correctly. When I did it again, I noticed that the green light next to the D was blinking too. I believe that one is for the transmission specifically, right?
Assuming that it goes based on the same long flashes for the first number and short for the second, it's giving me code 41.
Haven't been able to find a definite answer on what either of these codes are.
Really just trying to get some advice.
What are the codes and what should I do about them?

 
Rep Power: 367

some autoparts do read the codes for free

 
Rep Power: 134

Get the code checked with a scanner but most likely a transmission code based on your symptoms and the result of the jumper method you used. Best case is that it is just a faulty solenoid, switch or circuit. How many miles on the transmission?