I remember when I first started MTGO playing pauper goblins, I lost some amount of games to clock. And it was monored aggro. So, my hint here is: learn the commands first. Be familiar with your hotkeys, because now they will save you from getting timed out and even in the future they will save you tons of time. And in your example, don't just drop leagues.
In the beginning you will probably not get positive EV out of leagues. So you are actually playing $25 to play 6 or 7 rounds (25 is the challenge on saturday, which I recommend you not to play in the beginning, as it takes a lot more of time because of rounds and you probably won't get positive EV in the beginning) or $12 to play 5 rounds (leagues). So if you drop, you will actually be paying $25 to play 3 games instead of 6.
PS.: Triggers you always have a chance to respond (unless they are split second, obv). The thing about stops, is that in certain stops you can play something proactively. When a trigger goes to stack, you will always have a chance to respond it. The usual stops to maximize your time are:
Opp: upkeep, beginning of combat (unless they are playing that goblin that creates a token at beginning of combat, then you would have to have at main), end step;
Yours: Main, attack, block, main (end step is usually depending on the situation).
My advice is: focus on learning the UI. MTGO doesn't look modern, or anything like that, but for me it's the perfect way: is simulates a MTG match, just like in paper. And though it has some bugs, they are usually minor ones.
It isn't easy to get some value out of it, but it isn't hard also. Using the EV calculator at Goatbots.com, with 52% win rate you already have positive EV out of leagues. The prizes for tournaments are pretty nice, you can play whenever you want, don't have to interact if you don't feel like it, don't have to travel, wait for rounds (unless on challenge - but then you can wait watching some nice stuff on your computer), etc. Every program has it's bugs, and I don't recall MTGO having any major bug ATM (the only one that freaks me out is mindbreak trap not showing what you already have selected, I once lost because I had a bad mouse).
I don't know if you will, but I love playing vintage on MTGO.
PS.: If you don't have decks yet, these are my recommendations to building:
Search for archetypes
Bot chain (the best by far IMO)
Bot chain - not as good but can have a better price
Site with prices for tons of bots - This one has lots of other features too
Rarely, but sometimes it's got the best price