Haven't done it myself, but you're supposed to me able to get it all out at once. I think those that have say don't try it without a leveler attachement to your engine hoist.

When I did mine, it was with the body off, so different deal there. I have since swapped the tranny twice. Did those from underneath with a motorcyle jack and a second pair of arms. Kevin C has a trick with using ratchet straps through the open door windowns and down underneath to hold the tranny.

You putting the 5-spd back in? If so, changing the clutch in the process? My CF clutch did not come with an alignment tool. I got the clutch in first time on the stand using a universal. Unfortunately, the pilot bearing let go later so I had to pull the tranny/clutch from underneath. That time, I had trouble with the undersal tool. And of course you don't know that until you are underneath muscling the tranny back in.

Last point being, I had a parts tranny so I took the input shaft off it and made what is now the absolute perfect alignment tool. Let me know if you want to borrow it.