I'm trying to implement the attack on 3.5-Round IDEA and I stumbled with the initial pair generation step because they suggest generating $2^{32}$ pairs, which would normally be executed on a mainframe but I'm trying to implement it on my laptop (8GB RAM).
We know out of the top of our head that $2^{32}$ is 4 billion (32 bit computers can directly address 4 GiB, although usually only 2 GiB is available per application). That means you'll have to store things on disk, or more preferably a very fast SSD. If you want to address that then I would recommend binary tables and memory mapping, not streaming. Of course, the time it takes to perform lookups may still be too large. You might be able to add a smaller table in memory to perform a "pre-lookup" e.g. using a smaller hash over values or initial bytes.
I'm confused with the generation part so are there any papers talking about the pairs and if they are indeed normally executed on a Mainframe or not
Well, mainframe, generally you'd assume fast memory access for an attack to be practical (or at least closer to practical). So the memory needs to be there.
and in what mode they are ciphered
Attacks on the block cipher themselves are not using any mode, they use the block cipher directly. You'd use the most performant code possible, i.e. without all kinds of wrapping to implement modes and whatnot. If you just want to try stuff out then you can use a single ECB block without padding or even a single CBC block without padding and an all-zero IV (as the IV is XOR'ed with the first plaintext block in CBC mode, so you would just get the block encrypt again).
are they generally stored in txt files or in a database
No, you'd use a map in memory (RAM) or possibly on SSD, preferably one with fast access. Laptops would not be perfect for this as the SSD's are generally not that fast w.r.t random access, and they generally don't have any posiblity to store a second SSD.
and if there is a preferred initial key to encrypt with if you're trying the attack for the first time?
No, not unless you already know that the key structure has influence on the attack of course.