K2SE (K2 specifically) does a fuel rebalance on vehicles, and and introduces a new type of fuel that's used for most things. Does this play pretty nicely with the K2 fuel rebalancing and new fuel?

As far as I can tell, this mod does not adjust fuels at all, so shouldn't be a problem.

I have noticed that trains are very slow (this mod + K2); probably easiest to increase train power to compensate.

Also, the 250kg stack size is based on the assumption that a wagon should weigh 10 tonnes and has 40 stacks; K2 wagons have 60 stacks so the same calculation results in 167kg per stack.

I think you got it backwards :) Yes, I ended up using 250kg/stack, because it would nicely end up with a 10 tonne wagon, but... if a mod has 60 stacks per wagon, then 40 stacks should not weigh any less than the typical 40 stacks. The goal is not to end up at 10 tonnes, but at a reasonable weight per stack.

Having said that, feel free to adjust the stack weight in the mod variables :)

As for the original question, my mod does not rebalance fuel, so it probably works fine with K2.
The power of the train is based on the sum of the max-power ratings of the locomotives (in vanilla, it's 600kW, but it can be altered by mods, for various locomotive types), this value is multiplied by the fuel-multiplier.
The effect of fuel is based on the energy density (MJ/item) of the burnable item. It is capped though, so even ridiculous energy densities won't get you a lot faster than when using nuclear fuel cells.