Let's move the guide to this thread to prevent clutter.

skillfultree here wants the cannon Shuinsen, but not the other changes.
First things first. Download the modding tool Pack File Manager from here:

http://www.twcenter.net/forums/showthread.php?730823-PFM-4-1-2-Warhammer-support

Install it.

When its already installed, go to your Shogun 2 data folder (usually in C:\Program Files (x86)\Steam\steamapps\common\Total War SHOGUN 2\data)

Find this mod (AaA_S2TW_Naval_Unit_Pack_Mod). Copy the mod to somewhere else with another name (e.g. AaA_cannon_red_seal_ship). Open that mod file.

1. There, you'll find lots of directory. To delete something, click to a directory, then press del on your keyboard. The directory will change color to red, then click File>save to continue.

2. Delete everything EXCEPT the db directory

3. Open the db directory, delete every table EXCEPT the models_naval tables and units_stats_naval_table.

4. Open the units_stats_naval tables directory. You'll see 2 tables. Delete the nav and nvl unit_stats_table.

5. Open the van_units_stats_naval table. You'll see lots of naval units. Click the number, use shift or control to select all of them EXCEPT the Trade_Ship_Red_Seal_Ship. Delete them.

6. Fill the deck_1_top and deck_2 column with shogun_european_naval_cannon

7. Find the ship_crew_category, and change it to Galleon_Matchlock

8. Save, and done. Put it back to the data folder.