First time partial mashing...measured efficiency in the 40s?

So tried doing my first partial mash with my recently acquired 2 gallon cooler. While I did the iodine test and saw that I had conversion by not seeing any black marks. However, during the process I thought I had trouble with the actual temp of the mash. I felt the bottom was a lot warmer then in the middle.

Other then that, the wort was made with dry and liquid extract and beersmith thought my recipe should result in an OG of 1.052. As long as I had my temp right at hydrometer reading and read it right, I thought it looked a little above 1.040.

I should also add beersmith calculated this to be an effiency of 44.5%. I also made sure to preheat my cooler with water, had my LHBS mill the grains, and follwoed the strike temps beersmith gave me. I added the grains into the water in the cooler and tried stirring as much as possible.

Please ask any questions to help figure this out! I loved the process but just want to do it better next time.

Check the presets in the beer program. Lots of info to input such as wort loss, evaporation rate etc. Also, make sure you end with the same amount of pre and post volume. If you end with 6 gallons, but beersmith is calculating 5, your wort would be watered down. Ensure you are taking hydrometer readings at room temperature, you will get false readings (even "corrected") if the wort is too hot.

BTW, the recipe was the following:

1.7 kg Pale 2-Row
1.2 kg Light LME
.4 kg Light DME
.26 kg Biscuit Malt
.22 kg Crystal 45L

Beersmith assumed an estimated 72% efficiency would have resulted in a 1.052 going into the fermenter. I had something like 1.042 or .041

My mashing process consisted of mashing in a 2 gallon cooler. Beersmith produced the following mash profile for me according to my equipment:

Mash in: add 5300 L of water at 76 degrees C.
Drain mash tun
Batch sparge with 2 doses of 1.7 L at 75 degrees C.