Ok assuming you stay in city centre Malaga (for ease of transport access for your trips, bus and train).
If you were hiring a car, then you would do this differently, but public transport is improving a lot in Spain.
So you would have the evening to wander around Malaga when you arrive.
Lets say you loose a day on your two trips, then you got to Madrid at some point after your third night. Three full days in Madrid before the day you fly out.
It is NOT a bonkers plan. Also, I would certainly not take away any more nights from Madrid. I would work out how practical your trips are as day trips from Malaga, and let that guide you. Compared with options of basing yourself elsewhere.