As for ensuring that one print job doesn't start before you've reloaded the paper and pressed a button --> there's no provision for this. You will simply have to manually control this by not queueing the 2nd print job until you've loaded the paper ==> i.e. print odd pages; go down to printer and reload the printed pages; then go back to PC and print the even pages.
Not sure what you are saying the issue is, is this only one document with the issue or are all of your print-outs getting cut off? Be default the printer should be printing out the whole document, there is no setting that would tell it to stop half-way through the first page.
Are you connected with a USB cable? Is it longer than 10 feet? If it is, get a shorter cable and try that.