Am I really being efficient with my investments?

Consider this: You're a fairly active farmer, and you want to succeed at a faster rate than your friends. You think to yourself that perhaps there's an item that will enhance your harvest potential. Chances are, a side investment may hurt you in the long run unless you're dedicated to making it back. But realize that early on you're limited to small scale investments.

If you plant 20 trees that have a flat turnout or they don't provide anything for future recipes, you must take note, that in a few levels, the overall gain from the purchase may not be worth it. If you've played an MMO, you can parallel to buying an expensive level 18 sword that will help you get to level 20 in less than an hour. You'll lose half of your earnings just to realize that you could have bought the level 20 sword with better stats had you held on to your level 15 sword. Now you don't have enough for the level 20 sword and have to suffer 7 levels with lesser stats.

I recommend being on the safe side by progressing along the quest-line. However I can't assure you it's the best, because I haven't found out yet if new quests will be provided on leveling, or if the quest-line is a giant chain. But 9 out of 10 times, following a game's scaling quest-line will provide the best progression rate.

Another common interest is an additional well. I, personally, advise against it early on. Here's why:

Natural Water Rate:
1 water / 3 min.
30 water / 1.5 hr.
240 water / 12 hr.
Harvest rate: 3 min.

Well Rate:
10 water / 4 hr.
30 water / 12 hr.
Harvest Rate: 4 hr.

Overall, you can achieve a 1.125x water rate if you manage to harvest each water at perfect intervals. The true reason for a well is to be able to use an accumulated 30 and tap into an extra 10 for an implied 40. So if you're into planting crops like 4hr crops like wheat or vanilla when your field has expanded, perhaps accessing 40 or 50 isn't a bad idea.