The Perception skill check result needed to penetrate a mundane disguise can be increased to an arbitrary number with a sufficient number of assistants. Each untrained dude that aids another on the NPC's Disguise skill check has a 50% chance of increasing the NPC's Disguise skill check result by 2, and the NPC pays only 1 sp to get a day's work out of an unskilled hireling. (For example, 100 gp puts to work for 1 day one thousand untrained hirelings on the NPC's behalf and yields somewhere around a +500 bonus on the NPC's Disguise skill check.) The downside? Unless the NPC disposes of the hirelings afterward, they're in on the ruse. However, if the NPC dons the disguise far away from the point at which he's introduced, this shouldn't be an issue.
(Note that the GM determines how many folks can aid another on a particular skill check, so, really, a thousand assistants may be too many. If the campaign's already established that only, like, three assistants can aid another with a Disguise skill checks or something, there's this fine answer that'll let the NPC crank his Disguise skill check through the roof.)
A ring of mind shielding is 8,000 gp and stops lie detection and alignment detection magic. The ring has an abjuration aura so, until it's formally identified, it can be passed off as a ring of protection, and typical heroic PCs won't find it very useful if it's looted. If the NPC's other magic items need different aura, as the question mentions, the magic aura spell is probably the best route. Then it's just a matter of the NPC using the Bluff skill a lot.
Consider alternatives to this plot
In my experience, players are a paranoid and innovative lot. An NPC who wants to join the party for any length of time will arouse suspicion. The GM must assume that the players have consumed every narrative wherein someone new wants to join one or more protagonists in their quest only to have that someone new turn out to be an antagonist. Thus the players will resist this NPC joining their PCs.
Then, if the NPC insists, the GM must assume that the players have consumed every narrative wherein someone new is subjected to an interview or interrogation and that the players will use every trick to trip up the NPC. The PCs will likely subject the NPC to background checks and interviews worthy of a job at the Pentagon.
Then, assuming the NPC's façade hasn't cracked and the NPC joins the party, ultimately one of two things will happen.
- The PCs discern the NPC's ruse early. The PCs kill the NPC and take his stuff.
- The PCs don't discern the NPC's ruse. Because the players feel like their PCs did all they could to prevent this outcome, the players feel like the GM cheated, that the betrayal was inevitable, that their agency has been violated, and that the GM should go write a novel.
In other words, either way, the GM's plot occurs, but—also either way—no one's particularly happy about it. I offer below two alternatives to this plot, both of which I have used instead of having the NPC himself join the party.
- Have the NPC employ minions. Instead of endangering himself personally, have the NPC spend some cash or persuade some dupes to keep a distant yet careful eye on the PCs and report back. Or have the NPC hire a spy outright to infiltrate the PCs' ranks instead of the NPC doing it himself. (Note that the NPC can use a sending spell to communicate with his spy—it's very nearly undetectable on the target!)
- Have the NPC employ magical surveillance. A scrying spell on the PCs—or their mounts!—can often provide as much information as actually traveling with them. The spell greater scrying in particular has a duration measured in hours. Then, when the PCs have almost reached their goal, the NPC can teleport to the PCs' location and interfere.
Both methods are low-risk, high-reward strategies that don't see the NPC endangering himself directly. In fact, they're methods that reward the PCs' paranoia without spoiling the DM's plot. Further, in the case of minions, NPCs are introduced that, if not slain, can be used in later adventures.