Suppose your maximal integer size is 64 bit. Strings are not that useful for doing math in most languages, so disregard string types. Now choose an integer of half that size, i.e. 32 bit. An array of these can be interpreted as digits of a number in base 232. With these, you can do long addition and multiplication, just like you are used to with base 10 and pen and paper. In each elementary step, you combine two 32-bit quantities, to produce both a 32-bit result and possibly some carry. If you do the elementary operation in 64-bit arithmetic, you'll have both of these as part of a single 64-bit variable, which you'll then have to split into the 32-bit result digit (via bit mask or simple truncating cast) and the remaining carry (via bit shift).
Division is harder. But if the divisor is known, then you may get away with doing a division by constant using multiplication instead. Consider an example: division by 7. The inverse of 7 is 1/7=0.142857…. So you can multiply by that to obtain the same result. Obviously we don't want to do any floating point math here. But you can also simply multiply by 14286 then omit the last six digits of the result. This will be exactly the right result if your dividend is small enough. How small? Well, you compute x/7 as x*14286/100000, so the error will be x*(14286/100000 - 1/7)=x/350000 so you are on the safe side as long as x<350000. As long as the modulus in your RSA setup is known, i.e. as long as the key pair remains the same, you can use this approach to do integer division, and can also use that to compute the remainder. Remember to use base 232 instead of base 10, though, and check how many digits you need for the inverse constant.
There is an alternative you might want to consider, to do modulo reduction more easily, perhaps even if n is variable. Instead of expressing your remainders as numbers 0 through n-1, you could also use 21024-n through 21024-1. So if your initial number is smaller than 21024-n, you add n to convert to this new encoding. The benefit of this is that you can do the reduction step without performing any division at all. 21024 is equivalent to 21024-n in this setup, so an elementary modulo reduction would start by splitting some number into its lower 1024 bits and its higher rest. The higher rest will be right-shifted by 1024 bits (which is just a change in your array indexing), then multiplied by 21024-n and finally added to the lower part. You'll have to do this until you can be sure that the result has no more than 1024 bits. How often that is depends on n, so for fixed n you can precompute that (and for large n I'd expect it to be two reduction steps after addition but hree steps after multiplication, but please double-check that) whereas for variable n you'll have to check at runtime. At the very end, you can go back to the usual representation: if the result is not smaller than n, subtract n. All of this should work as described if n>2512. If not, i.e. if the top bit of your modulus is zero, then you might have to make further adjustments. Haven't thought this through, since I only used this approach for fixed moduli close to a power of two so far.
Now for that exponentiation. I very much suggest you do the binary approach for that. When computing xd, you start with x, x2=x*x, x4=x2*x2, x8=…, i.e. you compute all power-of-two exponents. You also maintain some intermediate result, which you initialize to one. In every step, if the corresponding bit is set in the exponent d, then you multiply the corresponding power into that intermediate result. So let's say you have d=11. Then you'd compute 1*x1*x2*x8 because d=11=1+2+8=10112. That way, you'll need only about 1024 multiplications max if your exponent has 512 bits. Half of them for the powers-of-two exponentiation, the other to combine the right powers of two. Every single multiplication in all of this should be immediately followed by a modulo reduction, to keep memory requirements low.
Note that the speed of the above exponentiation process will, in this simple form, depend on how many bits in d are actually set. So this might open up a side channel attack which might give an attacker access to information about d. But if you are worried about side channel attacks, then you really should have an expert develop your implementation, because I guess there might be more of those that I didn't think about.
