...yes, i wouldn't be concerned about the lining up of your printer, your desktop printer is probably not as accurate as the print providers equipment...
...I expect your piece of paper jumps about a bit when entering the machine and it probably prints slightly off center at the best of times, this is the nature of desktop printers really. If it has a proper duplexor it may do a better job, if it has a duplexor and is printing way off line it may be worth getting it serviced...
...when you select the text in the pdf, under edit > copy, is 'copy greyed out? if so then the document is protected by security features and no editing can be performed, unless you strip the security from the pdf via a password in acrobat professional or via third party software available to crack password protected pdf files...
Andrew