It's a bit unfair to compare a more expensive 4stroke engine for the 4*60 against an less expensive 2stroke for the 4*40. As its namesake suggests, the 60 will fly quite nicely with a .61 or .75 2stroke, which can be had for less than $100 - not much more than a .46.

As for the kit, the difference is around $20. Now there will be some incremental price increases in the accesories (e.g. bigger tank, more covering, etc.) but the differences aren't really all that great.

Unless you're just strapped for cash (in which case you should really rethink getting knee-deep in RC in the first place ), try not to let the price dictate your choice. IMHO, the larger 4*60 is the way to go, especially since you're already leaning toward it already.