Plugged into the built-in USB ports (the rear panel's ones)
[Edit] keyboard is plugged. Mouse is on bluetooth.
How is your El Capitan disk drive connected? Internal drive sled, external FireWire, external USB?
There are no common reports of issues with USB on Mac Pro 1,1/2,1 with El Capitan installed with Pikify.
Having said that, you could try an SMC reset (links in my signature below).
If that doesn’t help try booting into your Lion partition then navigate to /Volumes/yourElCapitanPartitionName/var/log have a look at the system.log file found there. Look for any obvious entries referring to USB.
Just out of interest, where did you get your copy of Install OS X El Capitan from? Is it an Apple sourced version, or did you pick it up off the general Internet? There are some versions floating around that are intended for the mobile-based systems (early minis, iMacs, MacBooks etc). Those systems that are based on the mobile motherboard are known to have issues with USB drivers and El C. There are some “patches” for those systems. It would be good to rule this out as a potential issue.
Do you have another machine you can use? If so, boot your MacPro into the El C partition. Use your other machine to remotely access the Mac Pro.
If your other machine is a Mac, you could use Screen Sharing, or secure shell (ssh) from the Terminal. Once you’re on the MacPro, use a Terminal to run the dmesg command (it’s the low-level kernel log output). See if you can spot any obvious USB messages here too.
Have you tried holding down the ALT key during boot (immediately after you hear the startup chime)? Does that do what it’s supposed to and put you into the boot partition chooser? Can you then use the arrow keys to move the selector around?
(You say the keyboard is okay in the Lion boot, which seems to rule out a hardware issue).
You could try booting El Capitan in “safe mode”. This will disable any none Apple Extensions. Boot into El Capitan, hold down the shift key immediately after you hear the boot chime.