Replacing the PGA Vref drivers with TL08 ICs fixed the previous problems. Tested all gain ranges by sweeping frequencies of sine and square inputs across the entire bandwidth, and monitoring the output on a scope. A function generator by Agilent was used to provide the input waveforms.

A simple laser cut enclosure was also made.

The picture below shows a 555 oscillator being studied using the device. Three oscilloscope channels are being used to monitor the output, voltage across the capacitor, and the midpoint voltage of the two resistors. The results are shown in the next picture.

Source: WIkipedia

I also started using the Input capture modules along with DMA to try to make a Logic Analyzer at no additional cost. Preliminary results from a TSOP1738 IR demodulator IC receiving the signal from a TV remote are shown

It was also used to test an SR-04 ultrasound based distance sensor

Without going into the details of scopes and logic analyzers, I'll post a couple of pictures of both monitoring the same signals.