no worries. when you disconnect the shifter from the trans it will be connected to the trans via little lever looking things there are 2. so when you had put the trans into 1 before you take off the shifter. then once off zip tie those little deals so they stay immobile. that way nothing moves when you take the intermediate housing from the trans. but if you pull the motor then you leave the trans where it is i assume so you would not have to do the zip tie. i guess you would only take off the bolts at the bell housing.
as far as pull the motor and do it that way if you have a engine lift and ever thing disconnect easy and what not i guess it would not be too bad.
i have installed and taken apart a trans 3 times in one day due to mistakes dumb moves. and the last time to get it back in and going took me about 1 hour 45 mins. so its not bad at all..
take a look at this this si what i used as a guide when i did mine very helpful.
http://classicbroncos.com/tech/clutch-replacement