How can I control selection on a PDF

I have Acrobat Pro 9 Pro build 9.4.6 and am constantly exporting documents from indesign to .pdf, and also building docs in the 'combine' feature from mixed pages. 
While everything seems to go reasonably well, I have a few problems that are due either to my ignorance, or bugs.
1.  The biggie; How can I control what I select, for the purpose of copying, moving and deleting?   When I drag the touch-up object tool over my selection, it selects what it wants to most of the time; sometimes it selects (i.e., puts a light blue box around) the entire page, instead of my selection (no pages are scanned).  There are very few instances when I get exactly what I want; there are usually a few lines above or below, no matter how careful I am in my selection.  The funny thing is that this is not a constant; sometimes, the tool works perfectly!  and I have my heart in my mouth every time I really need it to work, hoping that it will not force me to go back to Indesign to make minor corrections.   Perhaps my problems are connected to options I select when exporting my indds, but I've tried checking, clearing, and selecting various combinations and nothing seems to work.
Sometimes, the text selection tool is strange; a wide blue swath develops over the selected text, even though it is still usually possible to  edit the text in this condition.  And BTW, is there anything to do about the fact that some text can't be edited at all because a suitable font replacement can't be found?  Can't a font be added somehow that will take care of this?
2. Headers and Footers; fairly effortless, but if the footer contains two rows and I want them centered, the second row looks centered in the preview but not in the doc.  I have to go back to the footer dialog and guesstimate how many spaces to place before the second row to get it to look centered.  Also, is there any way to place a logo in a header?  That would be one of my requests for the next version of Acrobat, if not.
3.Hyperlinks; they don't always work,even though I check Hyperlinks in the Export settings.  Sometimes yes, sometimes no.
4.  Typwriter toolbar; it also seems to offer font and size changes whenever it feels like it, and I've tried all different orders of typing, selecting, etc.

It's me again, sorry!  I wanted to save what I'd written, and my message popped up to the board.
Thank you for any advice anyone has!
PS  My indd and acrobat are the same version, as they came in the same package (CS4).  Windows XP sp3.
Oh, one more thing I just remembered, as long as I'm complaining; sometimes if I place an object (the logo) and copy it to another page, it disappears on the original page, as if I've cut it.  Any fix for that?  (strange how I can edit tmy 'reply' but not my original post...well, at least I found where to ask a question fairly quickly!)

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