I reinstalled 3 times. On the third time I made sure that SH4 was installed by itself and then I added the U-boat missions. Next I applied Trigger Maru and the hotfixes for 1.9. No issues so far and thanks to the TMO crew for making a much better game. (On par with GWX? maybe....) On my first mission I was to go out to Hiroshima and take pictures of the harbor. Most of the water is really shallow near mainland japan. It was not easy. I sneaked in at night, sunk a carrier and crawled away from the destroyers to harbor and took some pictures. After some tense moments I escaped and made it all the way back to midway and ran out of fuel. I also forgot to save my game in all the excitement.
Oh well, I think I know what I'm going to be doing next. Also does the water do funny things on nvidia cards? Like skip a frame every once in a while with it being really noticeable on time compression? Also why is it that the all stop issued at the end of a course or when you resume a save game causes damage to your ship? I randomly seem to end up with damage whenever I resume a save.... Finally it seems that the steam version looks to me like a stock 1.3 dvd or something. That being said, there is no way to patch it outside of upgrading to the u-boat expansion. Also you cannot run the executable outside of steam (from what I can tell...launching sh4.exe also invokes steam...need to test this.....) I don't know if stock sh4 came this way, but if you click off the high res textures option, you'll find that a lot of 512x512 textures are missing for various objects like the colorado battleship. Sorry about all of that. Just thought I'd reply that yes, it all does work pretty well.
Oh and thanks! Didn't know that option existed in steam and that was precisely what I was looking for!