I realize this is several months later, but I'm possibly looking to doing this same thing. Looking through the adventures and reading reviews, it seems there is quite a lot of good here but also a lot of discontinuity for the story, and since there are so many different authors, a lot of the adventures run almost as stand-alone modules rather than a cohesive whole. But here is what I would do using the Nentir Vale:
1. Set Fallcrest as the starting town instead of Brindol. Reading the town's description in the 4e DMG, the south gate was never fully repaired from the Bloodspear Orc invasion, so that gives the opening attack of the town a legitimate way to happen. Ultimately, the town leadership cares a lot more about "Hightown" which is above the cliffs than they do about "Lowtown," so the lower part of the city is left with fewer guards. Eventually, the town's forces marshall and repel the attack, but not before a lot of damage is done and kidnappings have taken place.
2. Instead of goblinoids, use orcs as the villains, and have Sinruth be an upstart fashioning himself as a new Warchief of a new Bloodspear army. You can continue to use the orcs in the second module as well, especially if you find a way for Sinruth to escape and gather more forces. You could have him gain new "shadowy" abilities each encounter to emphasize that some more sinister enemy is behind him and granting him gifts of power. One of the 5e books had a lot of cool orc variants you could bring in to challenge players as they reach higher levels. I have also used npcs like scouts, spies, etc. and just said they were orc scouts, spies, or whatever.
3. There are a few options for the location of Rivenroar. You could use Kalton Manor, but the reason I am not is because I had another party of adventurers who did an adventure there and then rebuilt the place as their base. I had it a ruined keep instead of a manor. Lord Faren of Fallcrest awarded one of the PCs the title of Baron of that area and charged him with keeping an eye on the Witchlight Fens and the Harken Forest. But most people could use Kalton manor who aren't worried about that specific continuity in my world.
Personally, I'm going to put Rivenroar either in the Old Hills or the forest next to the Old Hills, which isn't given a name on the map. In the past, I have called it the "Wolfwood" and put the Wolf Runner bandits there from Threats to the Nentir Vale. They could become allies of the party since I run those bandits as "Robin Hood" style who happen to be led by a good aligned werewolf.
4. After the first adventure, I plan to have the party at level 3 and be given the opportunity to rebuild and use Rivenroar as a base of operations, with some downtime before the next adventure in the series to let players pursue personal goals and/or build up their base and meet local allies and enemies who might appreciate or not appreciate a new local ruler.
Beyond the first adventure, I haven't worked out where to locate Overlook and the other locations just yet, but I'm thinking about it. I plan to have Sarshan be the main villain, dropping the whole Githyanki invasion and Tiamat thing. I want it to be about Sarshan and his goal to cause chaos in the world and ultimately invade with his own forces from the Shadowfell/Elemental Chaos.