I have a 2008 with a T5 and noticed that sometimes reversed is blocked and I can;t get it into gear to backup, but if I tap the gas a little bit and rev it up to 1k or so it will suddenly open up. I don;t know if there's some sensor that only lets certain gears engage if the car is above a certain RPM but it's worth a shot to try it out.
I also noticed that 5th is blocked if you're coming out of 1st (I have no idea but I tried to shift from 1st to 5th one day and couldn't even though 40mph can be achieved in both of those gears). It sounds like there are some sensor issues that are telling the tranny not to engage certain gears or something. Sorry if this is not much help but I do have two suggestions:
1) buy a new tranny, there's actually takeoff GT trannys out there new for $700 bucks and install it yourself (the car already doesn't run so it should be OK for you to take the thing apart for a week or two and bust out the tools and get a book on tranny swaps)
2) if you are too busy to install the thing yourself, then you should be able to afford the install cost
Also, you can get a tranny from a totaled mustang in some junk yard for cheap, so if you install it yourself it could be like 200 bucks or so.