Cylinder three misfiring

So back in February, I was driving my vehicle and the transmission went out on it. Since this was the first thing to have gone wrong with it we decided to replace it with a brand new transmission. (Also we are still paying a loan on it so we were still paying on it and couldn't just let it go). About $4,000.00 later I got my car back and it had a brand new transmission. Then after driving it for about a week or two (which would have been the beginning of March), the check engine light came on. I had someone read the codes and it said my third cylinder was misfiring. I have now had the third cylinder "fixed" almost every month since then at the same location (taking it somewhere else will cause us to have to pay for the same repair that someone else didn't get the first time). It is due to go in later this week and there are concerns that this car isn't going to be able to be driven anymore. I didn't know if the transmission repair could have accidentally done something to the cylinder or if my car is just going to be unsalvageable at this point. It is just very concerning since the loan amount I have for my car is more than how much I bought it for and way more than what it is worth now. I didn't know if anyone had any ideas for why this could keep reoccurring or ideas of what we should do. Please let me know!