ok well let me break this bad boy down  

first off we need to have your wifi card model if you look at your first paragraph

I am having issues with network manager connecting me very slow, asking for re-authentication of the password multiple times and resetting my spoofed mac. I understand the mac is because they want me to enter a spoofed mac in network manager however this keeps it from logging on the network completely. I would switch to Wicd but that one drops me constantly and is a headache as well.

what does this says  about your card  ? also if you have both wicd install and network manager are both running at startup your card will not connect properly
regardless if your card has the right drivers etc etc

question why the shell  do you use the shell to connection to lan as well ?? don't get me wrong all aircrack is done in shell and connection but for a standard just connect hmm Im curious !! .. what are you doing or trying to achieve is it that you are just trying to do it by shell because network manger is not working for you ??

1 ) get your card model and check if the drivers come standard with linux wireless drivers or do you need to get them and compile them
1 ) can you connect to any access point with network manager # or is it just keep dropping i.e asking for re-auth { forget shell for the time being }
2 ) what is the status of rfkill ## things like this are just checks Not because this is what the problem is
3 ) iwconfig power  .. ## depending on your card power saving mode can cause problems with connection
4 ) signal strength
5 ) this AP is it yours, a company, etc etc

connection to wifi through shell you can do it off the cuff or if you can you can create a mywireless.sh and put your info and if you wanted create a start up script put the info into it and do update-rc.d wifi defaults


scanning AP
iwlist wlan0 scan | grep -e 'ESSID' -e 'Channel:' | sed 'N;s/\n/\t/'
you can use tr and some awk to clean it up if you want a bit more organized i.e strengh ,encryption on/off etc etc

connecting
iwconfig wlan0 essid {Network} key {Pasword}
dhclient wlan0

iwconfig will use hex as default if you want to use ASCII put 's:' before your the password

setup a static ip with dhcient.conf

So yeah if anyone can shed light on how to consistently connect to my AP through shell given I have the password key regardless of encryption that would be of help. Also if anyone has had a similar issue with network manager and knows a possible workaround to stabilize it.

again your card needs to be 100% compatible ,drivers,firmware etc etc ... and then back to the creating the script ..

some great points weVeg ..

I got a little confused of what he is doing and what is trying to achieve

If you install wicd, you have to remove network-manager from the rc.

I seen that but though surely he doesn't have both installed and if wicd is running in the background while your running network-manger
that is a recipe for disaster

USE either one or the other NOT both I would recommend Network-Manager

you can have two installed but only one running but the question is have two there is no need for it

but again even having two and only one running it may still cause a problem

100% correct Ive seen some people  SAY just install either network-manger or wicd and the one you install will remove the other this is completely  Wrong

Even after removing wicd or network-manager always check there is no startup files still operational