I'm not sure about the work needed or your abilities. Here is a link to your FSM:
http://www.nicoclub.com/FSM/Altima/1999/
here is a link to the manual transmission chapter:
http://www.nicoclub.com/service-manual? ... ma/1999/mt
Page 13 has the shifter diagram. It looks like you can get to it from the interior. But...
Because it sounds like yours is required transportation (work, school, food) I think you should take it to a clutch shop. Tell them what's up (gears pop out and change) and what you might suspect is up (maybe shifter is installed backwards). Let them rotate the stick (if needed), let them check the bolts and clutch and let them put it back together. You're not buying parts, so it shouldn't cost too much. They should be able to do it in a couple hours or less, depending on their schedule. Some places cost $100/ hour so ask for a quote first and be ready for maybe $100-$200 bucks. I think it should and could easily cost less than this, but everywhere is different. I wouldn't expect it to cost more.
Let me know if that's what you want to do. You could even print out the pictures or transmission chapter for them if they thought it was useful.