I was a bit slack with the transition from formula to cows milk. My DS stayed on the 6 + months formula (S26 Gold) until he was about 15 months. We did the transition over a fortnight, gradually reducing the number of scoops in the bottle. He wasn't too keen on the change in taste but didn't have any pains or different poo.

I don't think there is any harm in taking the transition slowly. I would decide if you want to transition to cows milk or toddler formula and just do that. It might be a bit much to transition onto toddler formula and THEN move onto cows milk.

The sickness could be coincidental or it could be caused by the changes.

If it was my son, I'd go back to whatever was working for a few days and then look at starting again.