I don't seem to be able to import more than 1000 rows when using PI Builder Element Search, is this a limitation or is there some configuration setting I can change
In Element search, request you to increase the maximum results more than 1000.
See if these steps helps you
Close the Excel
Open "PI System Explorer" then go Tools -> Options -> Genral tab
Change the value against "Maximum query size". By default you may be seeing 1000 there, so you may increase that value and press "Ok". Now open Excel and continue the Element search in PI Builder.
Retrieving data ...