1) Probably because those column names you are filtering with aren't unique in the query. Try updating the code by hand to use contactinStores.centerid and contactinStores.contactid and it will probably fix that problem.
2) it isn't a checkbox now... You may have adjusted the page so I'm not sure if you are still having issues with this portion.
3) this should be the default functionality. I think you aren't getting all the results because of your last select field not having the correct option value for the first option:
<select name="S_defaultstore" id="S_defaultstore">
<option selected="selected">All</option>
should be:
<select name="S_defaultstore" id="S_defaultstore">
<option value="" selected="selected">All</option>