'00' cougar 5-speed lost 2nd & 4th gear

Thanks to anyone that can help me.

I'm having lots of issues now with my cougar. This latest one is 2nd and 4th gear work like i'm in neutral. 1st, 3rd, 5th, and reverse seem to work normally.

Other issues that may have something to to with this is rough idles like the gas is being tapped repeatedly. Also when the heat is on I noticed a burnt oil/rubber smell.

Lastly and probably a seperate issue the car will shake violently when going about 50 miles an hour. I believe this to be alignment.

Sorry for the laundry list I'm hoping somebody out there can help.

**UPDATE**
Later that day I tried driving home and lost all of my gears. Some people are saying it might be transmission and others are saying it could be Linkage since I had some of the gears in the morning.

The shifter moves up and down but not sideways. It also doesn't seem to be connected to anything. I tried looking under the hood while my wife moved the shifter and heard a "wire scraping sound coming from a small 2x2 metal box. I can move the box left and right which in turn seems to shift the gears from 1st to 3rd??

I'm just wondering if I should be trying to drive it to a garage to fix or the scrap yard. :(

Does anyone have any ideas or thoughts on this?

Thanks