Search Record Issue

I have a script that searches a saved search that has up to 15000 inventory items.  I do one search which returns 1000 records.  Then I do another search that returns another 1000 items but excludes the previous items which are kept in an array.  When I try to do a third search, which would exclude the previous 2000 items, the script times out.  Is there limit for a search?  At times, the script doesn't time out, but most of the times, it does.
Is there a better way of doing this.
Part of my code is below.


// There are more filters
filters[2] = new nlobjSearchFilter( 'internalid', null, 'noneof', itemArray );