While there are many reasons that an export script may perform poorly I have found the following scenario to be fairly simple to correct:
Your custom export is saving image files out to a folder and performs well when exporting to a local folder but is much slower when exporting to network storage. This problem increases dramatically as the number of pages in the multipage image file increase.
If the above scenario describes yours, I have the answer for you. Open your export script and locate these lines of code:
These API calls perform exceptionally poorly when copying multipage image files to network storage. Alter your export script to use a local temporary working folder. When making the API calls to copy the files, use the local working folder path for the initial copy and then use standard windows file copy or move calls to put the file in its final destination.
I had a client exporting large documents and making this change reduced the export time from over 45 minutes per document to ~3 minutes per document. Needless to say, the client was very happy.