I think you could do two things. First, set another Mega as an Slave and make it do writes and reads on demand of the data input over serial. It's just to read the serial stream and put some switch case. This is the easier way better than custom making PCBs.
Option B could be to use some multiplexers. For example, one 8 channel multiplexer gives you a gain of 5 inputs, but, if you multiplex multiplexers (A,B,C from different ICs wired together) and select which multiplex use through another multiplexer it gives you the chance to control up to 64 pins with just 7 pins. Bad thing is you can only read or write 1 pin at a time. But, for example, it could help you with sensors or arrange stuff that is meant be "on" one at a time.
Now, if you run the multiplexing at a very high rate, it can't be perceived by human sense. So you could multiplex leds. Also, for solenoids, is possible to make a gate for them and make that gate stay until another signal is send.
Here's an example of how to set the pin for reading. So, all my sensors calls are made to the common pin, before this, I had a vector where I stored sensor pins and called it from a loop.
void multiplex(int pin){
switch (pin){
case 0:
digitalWrite(11, LOW);
digitalWrite(10, LOW);
digitalWrite(9, LOW);
break;
case 1:
digitalWrite(11, HIGH);
digitalWrite(10, LOW);
digitalWrite(9, LOW);
break;
case 2:
digitalWrite(11, LOW);
digitalWrite(10, HIGH);
digitalWrite(9, LOW);
break;
}
}
This is the way it is used
for (byte jtemp = 0; jtemp<3; jtemp++){ //lee los DHT
multiplex(jtemp);
int dht_res = DHT.read22(3); //3 is the common pin
}