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Flashing check engine light

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I was driving tonight and accelerating up a hill at about 3/4 throttle when my check engine light began flashing for about 20 seconds then left. after everything seemed to be fine however my transmission has always shifted a little rough downshifting. As this is my first car I just assumed this was normal. I drove a little bit later and tried a little Italian tune up. When at full throttle or near jt when my car is at about 4 thousand rpm it starts to jitter a bit like a little shake that feels like it’s from the transmission And the rpm’s flutter a little bit. I just replaced the engine about 2 months ago so I know it isn’t an issue with that. from a cold start when you first drive at about 20 km per hour a little click wound comes from the transmission and I can feel it through the gas pedal, I am now wondering if this was an early sign of my transmission failing. Does anyone have any thoughts or ideas as to what this could be. im so done with this car I have had nothing but problems with it but I can’t get rid of it cause it was my grandparents car. Anyone have any ideas what this issue could be?