Pilon Island: That doesn't seem like a great place to put a bridge. A rock of that size would be more of a hindrance than a help in building the bridge. Ships would have to stay *well* away from it, so the highest point of the bridge would have to be in between Pilon Island and the Mainland (or Pilon Island and Citadel Island), giving us an esthetically unpleasing asymmetrical arch. Two high arches is possible, but then we'd get get a big height difference across Citadel Island to link up with Highbridge.
It might be clearer if you draw the bridge in place as well, including the arches (for ship passage) and road surface. Even better: do it "backwards": draw the bridge
first, then figure out where the presence of such a rock in the river might be of help.
A secondary problem is that Pilon Island would also have gotten in the way in the pre-bridge era in the beginning of Mor's End's history. Such a rock in the middle would probably have made it a dangerous place to cross on horseback or swimming, not to mention driving wagons across a ford!
Docks: I highly doubt Mor's End would have that many piers sticking out into the river. Medieval river harbors mainly consisted of reinforced river banks where ships could pull up alongside. Piers are only necessary if you need to enlarge the amount of shoreline you have to dock ships at. Right now, the river bank in the main docks area (between the southern wall and Highbridge) is about 1200 feet long, which could easily fit 12 ships alongside it at any one time. Within that area, you've drawn about 30 piers sticking out into the river! That's one every 40 feet! You would barely have space for ships to fit in between...
Have a look at these closeups of some of the maps I posted earlier (caution: LARGE!):
Paris,
Dockum,
Maastricht,
Zwolle. In each case, the majority of the ships is simply moored perpendicular to the river bank, with hardly any pier structures to support them. Only on the Paris map are there a few structures sticking out into the river, but that one is on a very different scale from Mor's End (anyone know what the population size of Paris was in the 1500's?) I assume ships would only dock parallel to the river bank when they're actually loading or unloading cargo. In that case, we should have *plenty* of dock space without needing to build any piers.
Just for the fun of it, we may want to have one or two piers anyway. They're cool structures, and an interesting locale for a DM to place a combat, for example. Such a pier could easily be 100-200 feet in length and 15-20' wide, not like the small walkways you drew.
Keep your scale in mind when you're detailing the harbor area. That little ship icon may be way off scale for a three-master. In my current RP group we did a little research to commision our own ocean-worthy ship. It wound up being 25'x75', which is only barely long enough for a three-master. River barges may be narrower but longer. I'd say count perhaps 30'x100' for your average large ship, including maneuvering space around it.