Try this to get the pictures off the iPhone.
Open Image Capture, it's in your Applications folder, and with the iPhone connected, it will appear in the Devices pane.
From there it is reasonably easy to import the pictures to wherever you want on your Mac.
Not sure how you got the 2994 pictures onto the iPhone through iTunes, but remember that the sync process for music and photos, is one way. Mac to iPhone.
You may have to import the lot and then delete what you don't want.
As a matter of interest, what is special about your camera software?
How does it compare with iPhoto?
I would like to download all the photos taken on my iPhone onto to Macbook. I DO NOT have iPhoto on my laptop as it conflicts with my camera software.
I plugged in the phone last night via USB and iTunes came up. I clicked on the Photos tab and selected photos on the phone and which folder I wanted them to load into. What happened was the 2994 photos on my Mac loaded into the phone.
Now I have two problems - I can't figure out how to delete them off the phone or get the 300 photos on the phone onto my Mac.