On Morales' poor baserunning....
The way Fangraphs BsR works is that the run value of each base running event is summed up as the season goes along. For example, if a player is on second base and the batter hits a single, the baserunner is graded based on how often the average player scores in that particular situation. Morales scores less often from second on singles, advances to third from first less often on singles, scores less often on doubles, etc.
On a team like the Royals poor baserunning value is magnified because the Royals rely heavily on small-ball. They plunk singles for days, try to advance runners and keep the line moving, bunt, and when they get "the big hit" it's more than likely a double.
Toronto doesn't play like this. If Morales is on first base and Tulo or Martin swing for the downs with success then his baserunning is irrelevant. Morales' baserunning will be irrelevant on the Blue Jays a lot more often than it was on the Royals. So, don't expect his BsR to be as bad. But I can't quantify how much better it should be.
And on park factors....
Be careful when you say that Morales should be a better player because the Rogers Centre is a hitters park. It's true that his offensive numbers will be (or should be) better, but that probably won't make his hitting worth any more. That's not how park factors work. You would only expect him to actually be worth more if he has a certain skill-set that is specifically and personally catered to the environment.