I'd like a way to justify having 100 meter long guns be able to throw out 1-ton projectiles at 30 km/s or better
I don't understand your strange "tons", so lets use a nice easy measurement like a tonne. Your projectile will leave the barrel with a hefty $4.5*10^{11}$ joules of kinetic energy. If your coilgun only wastes 1% of that energy in heating the projectile, 4.5 gigajoules of energy will be absorbed by it (a little over the energy released by the detonation of a tonne of TNT, as it happens). The specific heat capacity of iron (for example) is 450 joules per kilo per degree, and it has a melting point of 1811K. From a starting point of a comfy 293K, it'll take $6.6*10^8$ joules to raise a tonne of iron to its melting point. The latent heat of fusion for iron is 247kJ/kg, or $2.47*10^8$ joules. You will note therefore that the energy required to melt a tonne of iron is an order of magnitude lower than that 1% waste heat.
In theory, then, your gun will explode immediately. You'll also find that you just heat your projectile up to its curie point and then you'll have real problems accelerating it further (or possibly at all), though I expect you'll still be able to heat it up just fine. Hopefully it won't hit the walls of your gun. Hopefully also your gun doesn't have problems with "dry firing"!
Problem one, then, the inductive heating of the projectile is gonna have to be hella low. Your coilgun is probably going to have to be >99% efficient.
Next, lets hazard a guess at the capabilities of your coilgun using a lazy trick from Luke Campbell (which I found on the ever-useful project rho). It isn't quite realistic, but it does give ballpark figures for the performance and plausibility of your magnetic guns.
Now assume that the barrel is filled with field, and that the projectile sweeps the field out of the barrel, turning the field energy into kinetic energy (this is not actually how coilguns work, but it gives the physical upper limit based on energy conservation). The energy density is about 400 kJ/m3/T2 times the square of the magnetic field strength (398,098 J/m3/T2 to six significant figures). Call this value K.
You now know the volume needed in the barrel based on how much energy the projectile ends up with
volume = kinetic energy / (K * (magnetic field)^2)
Lets imagine the barrel is 30cm across (a one tonne iron projectile would therefore be a little under 2m long). The swept volume of the projectile as it traverses a 100m barrel is therefore about 7.07 cubic metres.
Using the above formula, you're gonna need a magnetic field strength of 400T. That's a lot. This is waaaay above the magnetic saturation point for an iron projectile (1-2 tesla), higher even than the saturation point of a modern "high"-temperature superconductor (100-200T). You'll need to handwave greater-than-room-temperature superconductors to deal with that kind of field. Remember that if your field strength exceeds your superconductor's critical field the superconductivity goes away, and your gun will probably go bang, in a very bad way. Also remember that the dumb iron projectile mentioned above is a lot more tolerant of serious heating than your fancy superconductors, which will probably stop superconducting at much power temperatures than the curie point of iron. Your inductive heating requirements become even more stringent, which implies even greater efficiency required of an already stupendously efficient system.
Problem 2, then, is materials science. You're gonna need some absurdly optimistic super high temperature supercondutors to make this work.
(also, I hope you're just throwing dumb projectiles here. good luck getting any technology to survive the acceleration, heating and magnetic fields you're subjecting the projectile to here)
If they could get up to 100 km/s, that would be fantastic.
If by "fantastic" you mean "solidly within the realms of fantasy" then you're in luck! The energy levels you'll need to deal with are a good two orders of magnitude greater. Your superconductors and projectile will need to be made out of fairydust.
Problem three: you're already waaay out at the bleeding edge of what appears to be possible. You can't really go any further.
There are of course further problems related to the sheer amount of power you're going to have to throw at your gun to get it to boost the projectile to the required speed, the size and complexity of the associated ultracapacitor technology (which will go boom big time if damaged whilst charged!), the sheer amount of power your switches are going to have to handle in order to turn the acceleration coils on and off fast enough, the power generation requirements of your ship, the necessary heat rejection capability, and so on and so on. I think you're going to be disappointed, sorry.