As far as the bikes - how many bikes total are you trying to carry?
Couple of thoughts. First, one of the bolt-on fork mounts and a simple rear wheel tray could be made to work on the fender/running board area and wouldn't be much money but you have to consider the width of the handlebars on the bikes. Your handlebar in the pic is further out than the fenders, not really a problem on pavement but could be if you take the trailer down tighter trails. Limbs could really do a number on grips, brake and shifter cables.
Second, I think the most practical way to carry bikes would be to fab up mounts to put a set of crossbars over the cargo area of the trailer and then add the appropriate number of bike mounts to them. The bikes would be better protected from damage and you would still have access to the trailer bed for other cargo.