I just swapped my 89 auto to manual this summer, biggest things i found was:
need the manual transmission crossmember it will bolt straight to the same frame location
I had to do some form of running wires for reverse lights but i dont remember if it was because my wires were broken or not, regardless it was a 15 minutes task
I bypassed the neutral safety switch from the AT selector and placed a makeshift kill switch in its place
You will need to drill out the hole in the firewall for the master cylinder, there is a embossed section there it just has to be cut out, a series of drilling and a dremel works well
Clutch hard lines are easy to make if yours are in rough shape
The front panel on the transmission tunnel needs to be removed where the shifter sticks will come up, with this you also need to close the hole from the AT stick location
The biggest issue i had was the transfer case mount is about 2-3 inches further forward on the manual in comparison to the automatic, you can choose to cut it off the frame and move it or i make a flat plate that spanned the gap between the two locations and welded it so it would not rock under load, so far i have had no issues after bouncing it around the woods.
some things you may want to look at while doing it
I changed all the gaskets and seals on the transmission while it was out most can be found on partsouq but i had to make a few by hand
check all the rubber pieces on the sticks and make sure there aren't cracks, same with breather on the top of the transmission.
I would check your rear cam plugs too mine were cracked so i went to replace them while the trans was out as there really isn't any room to do otherwise (don't trust rock auto for them mine were wrong size)
For the installation
taking the shifter sticks off the transmission is how i got it out, and into the trucks this allows you to get it all the way into place and slide it forwards, you can reach all the bolts from the aforementioned hole in the trans tunnel. while you have that off its a easy time to take it all apart clean it and regrease it
The top bellhousing bolts you will need several feet of extensions and a swivel head to get them out (They are quite fun)
All in I bought OEM or the highest quality I could and ended up around 400-500 in parts as i replaced all the hydraulic components and clutches and had flywheel resurfaced. I was able to do the swap in a full day of work after having the donor transmission prepped and the pedal box and master cylinder placed in the truck before putting it on the lift and starting. It was my first time doing something like this and it honestly isn't as bad as i had expected just takes a bit of time and effort but its so worth it in my opinion. I gained a few MPG also between the swap which was a nice surprise. Feel free to message me with any questions about it.