Eric, either option works.
Using the numbers that I provided in an earlier post, it cost me about $90 apiece to get each cylinder sleeved. If you sleeve three cylinders, that's $270. And let's say your machinist will hone the other three for $25. That puts you at $295 if you have confirmed that you can reuse the pistons and that the other three cylinders are OK.
If you get all six sleeved, once again using my numbers, it will cost you $520 for the sleeve job and $125 for pistons for a total of $645. The difference is $350.
IMHO, the better way to go in the long term is to get all six cylinders sleeved and bored to standard. That basically gives you a new block that can be bored out four more times....020, .040, 060 and .080. That's the better long term approach.
But the long term approach has a price tag of $350. Is it worth it? That's an individual decision that only you can make.
I am running a '64 replacement block 261 bored .080 in my '57 3600. As others have stated, I would also be apprehensive about going with a .100 overbore. You will find posts on this forum advising against a .080 overbore, never mind .100. I'd probably sleeve after the .080 wore out instead of going .100. And, yes, I was aware of the advice against taking a 261 out to .080 when I made the decision to do it, but I did it anyway.
Let's say you get the three cylinders sleeved now to save money. Nothing wrong with that. Jerry or others with more expertise than me can advise as to whether or not the entire block can be resleeved the next time around with all new sleeves (meaning can the three resleeved cylinders get sleeved again?...and fresh sleeves in the cylinders not done). It might be a moot point for you depending on how long you plan to keep the truck, but it might give you peace of mind if you go the inexpensive route knowing that you or the next guy still has options to use the precious 261 block again. Or maybe the next guy can throw caution to the wind and have it bored .100...
Matt