Everyone changes things. The AP is a framework from which the GM further builds. You can run it as-is. But the truly enjoyable games are those which modify and alter things both to work with the players... and with the GM's own vision.
It's good to change things. I had Bruthazmus (RIP) take part in the Swallowtail Festival raid, and he met his doom. I created a sister for Titus Scarnetti, which created some cool scenes in my game yesterday, and probably more to come as I think she's having an affair with (still alive) Tsuto Kajitsu...
I'd say that changing stuff to personalise your campaign is almost always a positive. I've suffered when I've run stuff as-written that I didn't really like the look of. The APs have plenty continuity problems already, changing things won't break them - at most you generally just delete a later scene.
Maybe I should just run a homebrew campaign.
The main reason why I love AP's is that they provide the framework for an entire campaign which allows me to spend my time fleshing it out, customizing it for my players and our play style. The AP's exist to be altered and changed as you best see fit. Without them I'd spend all my time working on the big picture and wouldn't have time to make all of those great changes.
I've run two full AP's and I'm running a third right now. I've also played through one and the first book or two of two more since they first started coming out. Not one of them hasn't undergone all kinds of changes.
Follow the advice of others and make sure you read ahead so that you know none of your changes are being made to crucial elements of the story. Come to the boards to ask opinions on specific changes from those whom have played through the AP... but feel free to change away.
AP's are similar to the Pirate's Code: they're more like guidelines.
To the OP: everything you describe sounds like reasonable and appropriate DM activity and even encouraged - you want your players to buy into whatever AP you're running. Beyond the suggestion to read the entire AP before making changes, I'd encourage you to read other background material on Golarion and the Inner Sea. This should help you understand the history, culture, races and religions that are the expected backdrop of the AP. And help you see where and how you can change it.
Like for example, I've been toying with the fact of changing demographics in the places PCs go after knowing the party composition, so that they don't seem so out of place or something. Someone plays a tengu? Tengu enemies and commoners and stuff show up sometimes. Play a fetchling? You'll run into a community of fetchlings sooner or later. Nagaji? Expect them to show up sporadically when you fight enemies or go to taverns or whatnot. Goblin? I'd change things around so that you're not lynched on sight (although people may not like you). Not only that, I'd change things depending on backstory. Your character was nobility? Someone of a rival house is working with the bad guys. Mercenary? Run into merc buddies in your adventures. Basically, trying to help mold the AP so that it seems more...personal?
These all sound like good ideas to me. Personally I don't allow unlimited PC race choice, but if you do then integrating the chosen races into the setting seems like a great idea. A Goblin PC in Burnt Offerings could be fantastic and draw a lot of otherwise underused background info into play.
Re nobility, IMC one of the PCs is Kendra Deverin's oldest nephew, and would-be Deverin heir apparent. That created an immediate relationship web, and he's plotting against the rival Scarnettis right now. :)A common issue with Paizo APs is bringing the tons of tasty background info into actual play. Working to integrate your PCs into the setting, changing stuff as necessary to facilitate this, is a great way to bring out aspects that might otherwise go unseen.
NPC's that *could* cause you grief in later parts of the AP if you change them:
Aemiko *major plot hooks early - then nothing so if you do change and manage the hooks through the first book there is nothing to worry about*
Shelu *major plot hooks in book 3*
Aldern Foxglove *major plot hooks in book 2 - hard to resolve if changed*
The Scarnetti Family *very minor plot hooks in book 4*
The tunnels under the glassworks and dungeon under there *major plot hooks in book 5 - easy to adjust however if you change things just be aware*
Seriously that's all I can think of that really would play 'gotcha' if you changed them and didn't watch out for things in later adventures.
Overall of that small list of 5 the only one I'd avoid touching unless you want to seriously re-write an entire book is the 3rd. Considering the # of NPC's you meet up with and the scope of the adventure it's a pretty small list.
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Just to reiterate: Don't feel bad about changing stuff, that's your job.
Definitely read the whole thing first so you know what you're getting into, but APs on the whole are very resilient to tweaks like that.
For example, almost everyone's Sandpoint is completely different, because there's so much more material than you'd use in any one game. I've used around ten NPCs out of the dozens written up in Sandpoint. While both our games probably contain Father Zantus, he plays a very different role in my game because one of my PCs trained under him as an acolyte. Similarly, everyone's Shayliss Vinder ends up different.
So, you have to go in knowing that no two campaigns of Rise of the Runelords will be the same anyway. If you're concerned about some specific change, definitely come here, but I wouldn't worry about changing things on principle.
Cheers!
Landon