Some of these have already been ably answered but I'll just answer everything I know to summarize and so everything will be in one place:
a) For map contacts, BLUE denoted friendlies, GREEN denotes neutrals, and RED denotes enemies. Large boxes denote convoys. You will notice a difference in orientation of the icons for warships and merchants. Also, the "tail" sticking out the end denotes direction, i.e., the vessel will be moving in the opposite direction of the tail. Sorry, know some of this is obvious, but just want to be complete.
b) A GREEN carat means you have a GOOD gyro angle on the target. Your eel will not have to change course much coming out of the tube. In other words, you're lined right up in ideal firing position. YELLOW means your gyro angle is within acceptable limits for the torpedo. ORANGE means you are at the limit of acceptable gyro angle; you can fire, but I'd advise waiting. RED means you're outside gyro angle, check your stern tubes if you've got a bow tube selected or vice versa, you may be in angle from the other end.
c) Your torpedo tube problem sounds like a pain in the ass, but I'll give you what tips I can. Try following these steps:
FIRST, make sure your torpedo room has adequate, RESTED crew. If your crew are exhausted they're not going to get the job done very well, so move your red exclamation marks to quarters and get them rested up. Use as many qualified weapons officers and petty officers as possible, then fill up the rest of your slots with able seamen.
SECOND, if you have MANUAL RELOAD selected, you will need to go to your weapons officer, click on him, click your weapons management icon (the two torpedoes in the box), then you will need to find a torpedo in your reserves (it's all labeled in the window), click on that torpedo, then drag that torpedo over one of your empty tubes and hold it for a couple of secs. The torpedo icon in the reserve slot should then turn grey and if you hover the mouse over it it will give you a load time. You move eels from your external to your internals the same way.
If you have auto reload on, as someone suggested try rigging for silent running and then going back to normal routine, or even saving the game, exiting out, and reloading. I'd suggest in future always using auto loading unless you have some special eels and you want to save them and use them situationally or some other exceptional circumstance.
Worst case scenario is that this is a buglet and you're screwed, but I kinda think (and hope) not. Hope some of this helps.