I'm running it for 4 PCs, and none of them are controllers, so I'm eliminating a minion or two whenever possible.
The easiest thing to do is come up with your actual XP budget (based on 2 PCs) and rebuild the encounters around that, using the monsters available. So maybe the wyrmpriest isn't accompanied by 2 dragonshields, but by 3 minions; when the PCs enter the lair, Irontooth is alone; etc.
Yeah, figuring out the XP budget, like Klaus said, is a good step even if you do nothing else.
To do it the best "by the numbers" this is the best way to go
1) Find out your XP budget for 2 players of their level
2) See what the XP for each encounter is in the module
3) Start tweaking (remove creatures or replace them with deleveled versions of themselves)
I say this is best "by the numbers" because it has the potential to make the plot seem weird -- why is some particular villain lacking more backup support, etc. But if your players don't think that much in to it then I doubt they'll notice.
And also even with the right encounter mix "by the numbers" it's still easy for 2 PCs to get mobbed by large numbers. They'll be forced on the defensive much more than offensive.
Alt option 1: have each player run a second PC. But that depends on your group and play style as to whether or not that would be preferred.
Alt option 2: don't run the module. make up your own and use the module for inspiration if you want
Alt option 3: give 2-3 NPCs to join the PCs. But I dislike this idea, DMs have more than enough to do already, they don't need to babysit 2-3 extra NPCs every combat.
Alt option 4: (to be used sparingly or it gets old fast!) Slow down the enemy entry rate. For example, start the encounter with 1/3 the enemies in the zone. Then after 2 rounds, have another 1/3rd show up. And then, after another 2 rounds, have the final 1/3 show up... kind of like they called for backup during the fight. It helps keep the enemies a little spread so the PCs can handle a couple before being mobbed.
Alt option 5: (not my personal favorite, but, whatever) Make the PCs super strong (give them a higher pointbuy value to start with). Or keep them at standard point buy but make them higher level to start with. But in either case, the fact that it is still just 2 of them means they will be mobbed easily and also the proportion of actions that each side can take is skewed more than usual this way (in a 10 enemy fight; with 5 PCs that is 1 action on your side for every 2 against the PCs; but with 2 PCs that is 1 action on your side for every 5 actions against the PCs).
Random comment: It is often said that Keep on the Shadowfell is a deadly adventure for 5-6 PCs so even when remixing based on XP budget, remember that some encounters are just going to be plain old deadly even after proportionately lowering it.
It's late, sorry for any typeos and incoherent rambling. But hope it helps.
