The car crash flipper activation mech has the shortest travel of any coil/blade set I can think of - and I have a number of EMs in my collection. I've had to fiddle with it a few times over the last two years to keep it functioning well.
Seems like I'm a bit too late on this one - but I have an 08 Honday Fit - Gottlieb sys 3 is the only pre 95 machine that won't fit in it easily (have to take the head off, which is a major pain). Smaller SUVs beware on these... Mine is just a shade too narrow on the opening.
Flipper wise I've never noticed a wiggle during EOS - maybe tighten the allen screws underneath? It's a different feel cause it's a different maker, but nothing out of the ordinary. Coil stops will help the travel if that bothers you (I wouldn't recommend putting them significantly lower than intended). Yes, the coils are supposed to be different - you'll be thankful for that if you raise the inclination to max as Chun Li is basically impossible at that angle/original coil strength.
I've pulled mylar on two System 11s which are often hit or miss. All the articles and posts I read warned of System 3 Mylar so I've left mine alone.
When in doubt - especially on a Gottlieb... if you don't know the part number - just call Steve Young. He's crotchedy, but knows more than all of us combined and is the king of Gottlieb parts.