I have a 2001 350 Mag MPI w/ Bravo 3.
I think it is the same setup.
I have the repair manual which is good to have.
1) Basically, remove the serpentine belt by loosing the tension screw.
2) Then remove the bracket holding the impeller housing which is located on the front of the engine.
3) Once the bracket is off, mark the bracket.
4) Remove the 2 hoses going into the housing. Mark them, I installed them upside down once. Be ready to stuff a rag or wooden plug into hose coming from transom as some setups will siphon the raw water into the boat. It won't rush, but it will flow. Mine does.
5) Now you can take the whole assembly off boat to re-work it.
6) Undo plastic housing to get access. You should change the impeller, o-ring and housing as these housing being plastic tend to get worn. The impeller kit comes with just impeller or impeller and housing. I always do the full kit with housing.
7) Getting impeller in housing can be tricky. You can use some liquid soap if needed. Don't worry about direction of vanes, they correct themselves. Use a pair of pliers is needed to flatten and squeeze it in.
8) They say the bolts should be torqued to prevent from cracking the housing. I didn't do that first time, but then I bought a torque wrench for the next time. Just don't tighten them super tight, just hand tight, then snug with a socket is good if you don't have a torque wrench.
9) Re-assemble housing to bracket.
10) Attach hoses to housing.
11) Attach Bracket to engine.
12) Redo belt and re-tension to make snug.
13) Start engine and watch your temp to make sure its flowing. If you added soap you should see soap bubbles on water. If may take a minute or so, but don't go longer than a minute.
14) If on land you can do a visual for water flowing by drive, if in water, then you have to watch your temp, feel your risers, and hope!
15) One step I forgot was if you are missing a piece of your impeller, then you need to backflush the system to see if its caught anywhere. This is tricky as you have to remove a hose downstream and flush with water. Usually all pieces are in the housing.
Good luck!
PS. Looks like Mike beat me too it! Well, he is a pro, I am a amateur, follow him, but mine proves that anyone can do it! It's pretty easy.