Looking at fuel costs alone (excluding everything else):

Let's say the Focus gives you 50mpg average. At £1.37 per litre, you'll use £62 of diesel per week doing 500 miles, times 48 weeks commuting = £2975 per year

Let's say the Clio gives you 35mpg average. At £1.32 per litre, you'll use £85 of petrol per week, times 48 weeks = £4100 per year in fuel.

Obviously I'm making some assumptions about the commute in terms of how much will be flowing open road, and how much in stop/start town traffic.

The Clio might not need any expensive parts replacing when it starts getting used in anger for the commute, but who knows?

I would suggest getting a proper written quote for replacing the clutch on the Focus, and for fixing the brakes. Only then will you really know what the costs are going to be. Rough running may simply be the car needing a service.

That mileage is nothing - if you're doing 100 miles per day - the car is nice and warmed up - all incidental moisture burned out of the drive-train fluids - it should clock up double that mileage with standard servicing no probs. Aftermarket rear discs cost peanuts - an independant should do them cheaply - or do them yourself. Easy job.

I suspect with such a long journey you'll get bored in the Clio and might start thrashing it. Of course the Clio engine will be working much harder at fast A-Road and motorway speeds than the Focus one - therefore longevity would be similar - despite the initial higher mileage on the Focus. I wouldn't expect a small capacity engine to last much beyond 120K miles.