I did not use anything on my valve cover gaskets but had to fiddle to keep them lined up. As mentioned above, a contact cement would help here, the auto parts place should have some type of this designed for auto gaskets. I suggest a dab of RTV on the valve cover bolts to help keep them from working loose and to help seal them.
On the plenum I used Yamabond which is similar to hylomar. Only easier to find at your local Yamaha shop. RTV may work as well, but I habitually use Yamabond to seal machined joints on truck/car/bike/boat engines and have found it holds up really well. Some type of RTV is better on non machined joints, like the Rover oil pan since the Yamabond is really thin and will not fill large gaps.