It would help if you posted the version you are running. I have had no problems with ePub myself but usually use the web browser Send To Kindle. I have not experienced it taking that long unless there is a very large Table of Contents. Also it is the only format that provides Scribe with KFX personal document ('enhanced typography' features), and it seems likely other Kindles will start getting this at some point as well.
I presume you have access to the web browser send to Kindle?
https://www.amazon.com/sendtokindle (for US at least)
It supports up to 200 MB files.
It could be an issue with ePub formatting.