Welcome to Subsim & SH3
The manual will be in the documentation folder inside your SH3 Program folder. For what it's worth.
You can't jump directly to your patrol grid but you can go higher than 32. Be on the NAV map and crank the TC upto 1024. This is the max in stock SH3.
The red
! means that your men are fatigued. You need to swap them around with fresh crew members from the crew rooms. When transiting to your patrol grid, only have the minimum of crew on duty so that you have fresh men for when it counts.
"Unable to comply" this is because your crew in the engine room are to tired to maintain the engines. Again, replace with fresh crew.
As for getting cfg/code changes, you're are at the best resource right here at Subsim.
There are many mods available here and most have been put into Supermod packages but for the time being, find your feet in stock SH3 and then look at a package to suit your playing style.
Have a look here for the list of modifications, apart from the engine code (which is not moddable without an SDK) there is no area of SH3 which has not been tweaked.
http://www.subsim.com/radioroom/showthread.php?t=78792