Those two holes in the top rear portion of the long exhaust housing are not actual water outlet tell-tale holes. there is a inner exhaust tube/housing within that long housing, the purpose of which is to fill with water between the two to cool that long section... otherwise, the paint would burn off during its very first run. When that area fills with water, the excess spills out those two holes. If not for this setup, you can see that the water would continue to rise to enter the bottom cylinder at a minimum.
I don't remember if that engine has one or two water tubes, however.... The water tube rubber grommets are installed into the top of the water pump "underneath" that small metal or plastic bracket that's screwed/attached to the top of the pump. Keeping in mind where the grommets are... the tube(s) should enter them fully.
You can tell whether you bent the tube(s) or not by doing the following: From the section of that long exhaust housing where the lower unit attaches (the edge of it)... measure from there up to the bottom of the tube(s). Now, measure from the top surface of the lower unit up the pump to the height of that measurement... that's where the bottom of the water tube would rest within the pump when it's assembled.
If the tube(s) is bent... you can't hurt it any further and it's one hellava job to change (remove powerhead/adapter plate, etc etc... quite involved).... grab it with long nose pliers (or something) and pull it down if you can (it can be done).
The nylon guide(s) are always on the copper water tubes, BUT they vibrate up the tubes as the engine runs, then salt corrosion does its little gluing job and hides therm quite well. Look closely up the tube with a strong beamed flashlight and use a long junk regular (slotted) screwdriver that you can put a small hook in the end yank it/them down.
That small bracket that screwed into the top of the water pump has a ridge when the water tube goes.... the ridge is to hold the guides in the pump while you guide the lower unit upwards so that you have a good view of the tube(s) entering the guides.
Next time, when you're not sure of what you're doing.... ask here first.