As for where your game is installed, Windows "protects" the Program Files folders from alteration if it doesn't come through a Windows "certified" app, which JSGME is an old WinXP app. Therefore, 'modern' versions of Windows will roll back most of the mods' file changes. If you want to do mods to the Stock game (most folks do), you should move the game's folder. If you have a 2nd hard drive, you can create a Library folder there, using the Steam App on your computer, and put another copy there. I made a post a while back about
Moving Steam Apps, and that has the Steam App way, with a link to the Steam forum where both the Steam App way, and the Manual Method of doing it are discussed, which you would have to to the manual method if you have just one hard drive, like most laptops do. I've got my SH3 and SH5 Steam apps installed to "D:\Games\", and Steam adds all of the folder structure below that for the games. If you move the current install, you should de-activate all mods before you do the move, and you might also have to delete the JSGME.ini file in the game folder, and the same file in the MODS folder, so that it generates new versions with the correct "path" for the game's install. Don't mess with those unless you have to though.
The "stuttering" problem you describe is the same in the SH series, and has more to do with Campaign structure than anything. The game engine can only do so much. In SH3, the whole game loads as it starts, so you can ~really~ slow down in it, but they didn't do the HarborTraffic as thick, like they did in SH4. Some of the "layers" in SH4 span the entire war, while others only run for a year of so of time. The ones that run the entire war are what cause most of the "stutter" near harbors. If you've got 35 groups set to spawn every 900 hours (37.5 days), at a 35% rate, that's still over 3 groups for each of the 35, each year, or a total of over 119 groups. Most of those do not "terminate", or go away. So by 1944, you would have almost 240 groups in that harbor area, all vying for the same water. Osaka Bay on the Inland Sea is like that, and it actually has quite a bit more than 35 RGG there. I'm sure Tokyo Bay is worse.
In spite of issues like that, the game is a blast. It might just be that you've got partially activated mods, and the game isn't running at its best in the Program Files folder. Moving it might improve things. You could also try Fall of the Rising Sun Ultimate, and see if it runs better for you in those areas, but even if you don't, just reduce your TC in the harbor areas, and enjoy the game for what it is, which it is now almost 12 years old officially, but actually, counting the SH3 underpinnings, over 15 years old. It really doesn't do too bad for something that old - "old" as defined by computer life spans, and not human. We could explain how far your boat would travel at a given TC setting, and why you should reduce it, but I've bored everybody enough already...
