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setup_ccp3(CCP_PWM | CCP_PULSE_STEERING_B);

This would be selecting PIN_E1. You would also need to set the TRIS for port E to make PIN_E1 an output.
The data sheet shows Pin B0 has no h ...

You can't use separate setup_ccp3 statements. You have to OR the setup options together in one setup_ccp3 command.

Are you sure your sensor data is in the correct float format?

If you need to provide an external signal to clock Timer0 then pick a pin that is not being used. The default pin for T0CK is RA4. Feed that with a TTL/CMOS level signal from some external source.

Don't use T0CK at all.
Don't clock timer0 from an external pin.

Timer0 can be clocked from the internal instruction clock or from an external pin. You are choosing an external pin and then trying to set that external pin as the ceramic resonator oscillator input ...

Why are you setting pin A7 as the T0CK pin? This is one of the pins the ceramic resonator should be connected to.

What are you using to drive Timer 0 input?

Instead of connecting your encoder to the T13CKI pin can you connect it to an interrupt pin? This would make it easier. What pin does your encoder direction signal go to?

I believe the 16C55 used parallel programming instead of the serial programming so new serial only programmers will not work.

bulut_01,
Where did you get your repeated references to UART and KEELOQ from?

You have made a lot of statements about what you have for hardware. Many of those don't seem accurate. Only you know what you have, or maybe you are not even sure.

When you read the pin state, toggle a different output pin. Look at both the input pin and output pin on a logic analyzer to see if you are sampling at the correct time in the bit.

The reason Manchester encoding exists and why it is used is that the clock is imbedded in the data. You don't have to know the exact clock or bit rate you just have to be somewhat close (+/- 20%). T ...

On your logic capture, remove the UART decoding as it is invalid and is causing confusion.