Pagination of the repeater field is something that is on the to do list of the plugin’s author and will be making it into the plugin sometime soon(we do not have a timeline yet).
Regarding the issue at hand, it is recommended to make use of Custom Post type to breakdown the structure of the repeater so that the values can be entered on different pages. This will ease the timeout issues once the number of rows peaks.
I hope this info helps!
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