Recording 2 simultaneous tracks sustain pedal problems

That sound more like a buggy midi editing problem. I've often have midi events go wacky for no reasons and thank goodness for undo!!

   Instead of making a copy of the midi track. Send the output of the corrected midi track to the first plug and record it. Then change the output of the midi track to the second plug and record that. They should be in perfect sync.
   Should be...
   Hope it works out. I also love to blend two piano sounds.

   If you loaded the synth as a simple instrument track, right click on it and select split instrument track. Then you will have an audio track for the synth and a midi track that drives it. At the bottom of the inspector are the tabs for selecting inputs and outputs.
   After you split the track select the resulting midi track. Then you can set its output to any available midi out or loaded synth. 

My standard "piano" sound is a combination of layered acoustic and electric pianos. Both happen to be from hardware synths, but it shouldn't make much difference to the following.
 
What you want to do is arm only one of the MIDI/Instrument tracks to record, and after recording, Ctrl+Shift+drag-copy the recorded MIDI to the other track with 'Copy Entire Clips as Linked Clips' enabled in preferences. Shift constrains the time so the copy remains aligned. The linked clips will be indicated by dotted lines around their perimeters. With linked clips, any edit you make in one clip is automatically applied to all others (the clips are really just pointers to one set of MIDI events in memory).
 
Taking this approach should eliminate a lot of your issues. But I do enough editing of piano recordings with lots of sustain (also using soft synths sometimes) to know that it's likely the issues you encountered were largely self-inflicted, though it's difficult to say exactly what you might have done wrong. One way or another, it sounds like you moved the controllers independently of notes such that the pedal down was occurring after the note(s) had already ended.
 
One thing to watch out for is when quantizing, be sure to leave 'Only Notes and Lyrics' checked to exclude Controllers. Quantizing sustain events can make bad things happen, especially if you ever quantize to 100%.
 
On the other hand, you'll want to make sure to enable 'Select Controllers Along with Notes' in the Controllers tab of the PRV so that pedal events maintain their positions relative to notes when you drag the notes.