Yes, engine and trans install and remove separately. They TIV motor is much tighter of a fit than the T1 due to length, so while you can remove a T1 engine without loosening the transaxle (although its s easier to loosen it) you will likely have to do this for a TIV motor.
A few additional notes to what was written above by others:
Not all shock tower cross braces are removable. If it is removable, remove it, but if not don't worry it went in there that way and it'll come out, just tighter fit.
We do not remove our clamshells for engine/trans install. I just tie it back, slightly over center, with a rope from the passenger side striker bracket to the battery tray after the exhaust is removed. You can remove it, but I find it unnecessary.
Likewise, we do not remove anything from the motor, other than external connections (oil lines, wiring, throttle cable, fuel lines) we install and remove them 100% intact otherwise. HOWEVER, you may need to remove your crank pulley on a TIV. It's been too long since I've done one, but I know it is a lot closer tot he torsion bar tube than a T1. you may find it easier to remove alt pulley or air cleaners as mentioned above, and extra space helps, but it is unnecessary and will go without them removed.
When coming out (or going in) it is all about the angles. Walk it off the input shaft and start tipping the fan shroud towards the rear of the car. You'll wind up with about 30* angle front to back and then once you're off your lower studs you'll start tipping the driver's side head upwards and will wind up without 30* angle left to right also.