Don't know about the brake hoses, but the rubbing of the tyres can be fixed by relocating and reshaping the rods, I suppose it is brake reaction stays you are talking about. You can losen the lower end of the stay and put some washers between the stay and the chassis. In that way the stay is lifted a little up and away from the tyre. You gain only a few mm, but it might be enough. Another trick is to take the stay out, put it in a vice and then gently squeeze/deform the part where it touches the tyre. You should get an elliptical cross-section, with the smaller diameter perpendicular to the rubbing point. That will give you a few mm more, or you could use both tricks in combination. Of course that will not solve your fender or brake hose problem. Is it possible to reroute the hoses? At any rate, it should not be too serious. If the stay and the hose just touch, there should not be much or any at all chafing, but of course you should inspect from time to time.
If you choose to take the stay out, take care not to get any misalignment when you remove the top bolt, i can be difficult to enter the bolt again.
