A very small delay isn't really a problem. The chip is currently sampling each input at over 300,000 times per second but it wouldn't really matter if it were only 100 times per second. I can't imagine the cap would add a delay much longer than that.

I might be able to solder the capacitors under the PCB and the 2K-R12 resistor would have to be on the wire but since that's in series it's position shouldn't matter.

I don't think any of the spikes go high enough to cause a problem with the PIC. I've never seen one get up to 3.3V. The negative ones may be a problem though.

Thanks for your help. I'll try the extra cap/resistor as it looks to be a simple mod and see what the Oscope looks like.