don't forget electrical... the computer might not like the 5-speed, even though the trans has it's own separate computer the engine computer still gets data from the trans and if it stops getting that data it will throw a CEL that can't easily be removed... the easy solution would be to swap out for a ECM that was originally designed for that motor with a manual trans
also electrical connectors on the trans.. manual transmissions typically have a reverse sensor (for turning on reverse lamps) a speed sensor (for your speedo), and depending on other stuff it might also have a reverse lockout (to prevent you from shifting into reverse while driving) among other things.
Also a Manual ecu might want a clutch pedal switch to determine when you're using the clutch, though a lot of times this is just used to start the car and can be tied to ground to fool the computer into thinking that you've always got the clutch pedal in.
if you're getting the trans from a junk yard it might not be a bad idea to snip off all these connectors and take them with you. I konw on transmissions swaps I've helped with in the past I was able to call a dealership and get "pigtails" for all of the connectors I needed , which are essentially the plug with a few inches of wire that I could use to build the harness myself... these aren't always cheap though. usually $15+ per connector, might be more for something like an Isuzu though.
then there is other stuff like the clutch line, any mounting brackets you might need...
most times the bolts used for the automatic flywheel wont work with the manual trans flywheel...
little crap like that can add up an add up fast, but thinking about it beforehand can save you some coin, especially if you've got a junk yard with a donor vehicle.