I see two problems, one is actually a bug, the other one can be fixed quickly.
1. The results limit is set to 1000, which is extremely high. For large result sets wordpress will have to parse up to 1000 items before returning, which takes a long long time. The search process finishes quickly, but the post process of getting all of the post objects takes a long time. Another problem is that the isotope front-end scripts gets swamped by this huge amount of data, and it can cause the customer browser to freeze.
I rather recommend setting the limit to a maximum of 50, it's more than enough for ajax results, people tend not to look farther than 20 items anyways. The best possible configuration is to have 10-15 results in the ajax list, and displaying the “more results” link on the bottom, which redirects the customer to the non-ajax results page, which is limited to over 500 items, but displays only a handful per page – conserving the performance.
2. There is a known bug with filtering the same custom field with two different filters, which I though I have fixed with the current release, but it didn't work, sorry about that. This will be fixed within the upcoming release.
I would also rather suggest using the range slider for this filtering, it's much lighter for the database, as only a single “BETWEEN” operation is executed to get the correct custom field values.
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