Like you, I didn't know all of the stock manipulating tricks until after I completed the game. It bothered me enough that I replayed most of the game in order to finish with over $2 billion. If I knew then what I know now, I wouldn't have started over. Not because there is nothing to spend the money on but because I have found a reliable method to accrue money after finishing the main story. Although there is a cap on how much money you can have at any given time, there is no such limit to the amount you can invest in a given stock, so long as you don't go over the $2.1 billion mark in shares of a stock you own.
At the moment, I have about $320 billion invested in BAWSAQ stocks. Why would I need that much money? The zombie apocalypse of course...dummy.
Anyway, almost all of this was accumulated in the same manner. Although it is claimed that the BAWSAQ exchange is based on the activities of online players, I don't believe it. If you watch the bawsaq exchange long enough, you will see fairly predictable trends in certain penny stocks. You will notice that certain stocks drop substantially for a few days and then rebound. Focusing on 3 or 4 penny stocks can net you 50% to 200% returns over the course of a few days. Every once in a while, you will see a stock go from $2 a share to $15-20. I'll take a 1000% return all day.
I've also found that designating 8-10 save games slots for different point in the trading process come in handy for those times when you were wrong about a stock.
I got tired of typing my original reply, but I had a good night's sleep and my morning coffee, so I'll add a few tips:
Stick to stocks valued at $0-4 a share. It is much more likely that a stock will jump from $4 to $8 than it is to jump from $50 to $100... at least in GTA.
Stick to BAWSAQ, it is much more volatile in the short term, which is what you want in this case.
Snap photos with your phone (real, not in game) of stock prices on a daily basis for a week or so. It really helps with identifying trends. Don't pay any attention to the 5 hour highs and lows. They are garbage.
Finally, I noticed that although certain stocks tend to follow a pattern, that doesn't seem to be the case in the long run. They seem to go up and down over the course of a month or so and then the pattern changes. For this and other reasons, save often and save with different mixes of stocks.
Thinking back though, I typically would roll back to a save point not because a stock tanked but because I sold it at a 30% gain when I could have sold it after a 60% gain. At some point, it isn't fun anymore. Trying to move 50 billion between stocks when the limit per transaction is 2.1 billion isn't worth it.