Have you talked to Jonathan and/or your PT about whether your injuries had anything to do with your SPD pedals? Your knees didn't give you any issue last fall if I recall, so I'm not sure of the connection, but it's something you should talk to them about. You've been clipping in in spin class without incident this winter, right?

I tend to think you'd be better off putting your SPD pedals on now when your mileage and average ride is still pretty low/short than to decide in the middle of summer that you want to go back to them. T But I wasn't as convinced as you were that your pedals were the real culprit last summer. They may have contributed to the extent you suddenly started engaging your muscles in a new way AND riding over 150 miles a week, but that's why it might make more sense to begin using them now when your riding volume is still pretty low. Give you muscles a chance to acclimate, but take them off at the FIRST sign of any problem.

Has Jonathan ever suggested Andy Pruitt's book The Complete Medical Guide for Cyclists? You might want to get a copy of it for reference.