While fuel pump gets my vote (see post #2), a couple of posts in this thread have suggested the secondary shaft nut in the transmission since this is an early VIN. While I DO AGREE that you should separately address that, I don't believe it is the source of your noise.
Inside the transmission case lie 2 parallel shafts loaded up with gears that get meshed together to give the necessary combinations of speeds. These two shafts run end to end and and each is held in place with a big nut on a threaded end. Well, someone in the Renault(?) plant got lazy and on a bunch of the early VINs didn't do the final step when tightening the nut down. He was supposed to hammer the nut's collar against a small flat on the shaft, thus preventing the nut from ever backing off. By not doing so, he has allowed many of these nuts to ever so slowly start spinning off with normal use of the transmission. Soon the shaft gets a little bit of play, for and aft. I believe this contributes to the symptoms of making it harder to shift into second gear as the little bit of play misaligns things a bit and the weak roll pin gets extra stress on it. Ultimately what happens is the nut starts carving a groove in the back part of the relatively soft aluminum cover and one good shift later, the shaft moves enough to crack the case open. Whether related or not (I'm sure it is), also check springs that may get chewed up as a result of things not quite being aligned correctly any more. Ask me how I know this..
So, concentrate on the fuel pump/rubber sound boot/accumulator, but pay very close attention to any change in your shifter feel. Whether you go in proactively just for that or take the opportunity to change the clutch, perhaps add drive shaft sleeves or whatever else needs doing under there, I would plan on doing that for peace of mind.