Joe,
The truck side frames are EMD and not GE. The ones on your locomotive are closer to HT-C trucks which replaced the older Flexcoil design. Here some nice images from another modeling site of HT-C trucks. The HT-C truck was developed in 1970-1971 and was standard on dash-2 six axle EMD trucks like the SD40-2, SD45-2, or the much maligned SDP40F.
Your SD45 should have Flexcoil trucks. SP did have the SD45X model with was a test bed for the HT-C truck. See this link for a photo. However, you can also see, this not nearly a stock SD45.
The stock SP SD45 is shown here with the Flexcoil trucks. The good news for you is that if Atlas is using the same truck block as MTH, you can swap the side frames out from say a Railking FP45 to get something closer to the prototype. I am planning on going the other direction and putting HT-C side frames on my two MTH Amtrak FP45s as a first step to getting them closer to the SDP40Fs they are meant to represent.
I saw your other post and didn't want to comment as I didn't want to start a flame war unnecessarily. I hope you are able to get the final results you are looking for as that old MTH tooling that dates back to Weaver with a true fixed pilot in two-rail is not too bad looking. With the correct side frames, I think you have a pretty credible SD45. Best of luck!