And you are using each one of the images as an individual source, edited individually to the timeline instead of ingesting them as an image sequence?
Make a new, empty sequence File > New > Sequence
Click ok to whatever sequence settings are offered to you.
Drag the first image of the image sequence to the timeline. You will be asked if you want to Change the sequence to match the clips settings. Click on the Change Sequence Settings button.
Load the remaining clips to the timeline. You should now have a sequence with all your images that needs to be rotated 90 degrees.
Make another new, empty sequence File > New > Sequence.
This time, when the Sequence Settings Pane appears click on the Settings tab and set the pixel dimensions to 3296 x 2544 and set the frame rate you want. Click OK.
Go to Preferences > Media and set Default Media Scaling to none. Click OK.
Drag into the empty timeline the sequence that you had just previously made (the one with all the images but in the vertical orientation). It should appear in the timeline as a solid green bar. When you are offered to match sequence settings, click on keep existing settings.
Click on the nested sequence that you have in your timeline, then once selected, go to the Effect Controls panel and rotate the image.
You should now have a sequence with the images in the correct orientation.
MtD