I have done this more time than I care to count, so I will try and add a few tips not already said, (great stuff) for this and a few other issues regarding pulling the 5 speed.
If you encounter super tight bolts at the top of the bell housing and have an issue with the head of the passenger side top bolt, rounding over, the fastest and easiest solution I have found is grinding the head off.
This can be done by removing water heater hoses, and harness from the passenger side. There are a couple of big connectors and the drop for the oxygen sensor. Stock, there is a plate at the top of the bell housing that holds the connectors. Remove the oxygen sensor from the passenger front exhaust and remove from harness below before removing the harness above. You probably already have that removed if you are reading this.
On a Mach 1 or Cobra the connector line is folded over the release, thank you for that Ford. I just pop that off with a screwdriver and break the attachment point and use a tie down to secure later. Remove the windshield wipers, the plastic that wraps the bottom of the hood, windshield, and the plastic curved tray that wraps the top of the fire wall. There will be metal lip made of spot welded metal protruding off the top of the full length of the top of the fire wall. Some of these have an additional metal ledge that sticks out even further right above the heater core pipes protruding. If this is the case, bend it straight down with some vise grips and bend it back later. With the harness removed and out of the way on that side, exhaust pipes removed, drive shaft removed, and cross member removed, stick removed, battery and started removed, jack up the tail of the 5 speed as far as it will go up into the tunnel.
Now hit the hardware store and buy a 12 extension for wood bits. Vermont American makes them and they are about 7 bucks. Pick up 3 grinding wheels that are about 1” in diameter and about 1 ½ tall. Get some decent Vice Grips and grab 2 of the washers from the already extracted 2 rear exhaust pipe flanges, and clamp them on the edge very tightly right above the bolt head we want to grind off, with the opening of the washers over the edge of the metal lip that runs the length of the top of the fire wall. Grab a drill and grease for the shaft of the extension, ‘cause you’re going to need it. Feed the shaft through the clamped guide washers and attach to drill. Grind away. It can be done with 2 wheels, but 3 is usually required for first timers. It takes some finesse and about an hour of continuous grinding. When you pull the 5 speed later you will be able to remove the stud with your fingertips. No engine pulled, no intake pulled!!! Keep in mind that 32 valve heads cause the engine to tilt less and so fairly straight access to the top bell housing bolts is not achievable as with the 16 valve models. The little bit of difference is the difference between being easily able to extract the top bolts with extensions and a universal from the rear, regardless of how tight the bolts are, to almost impossible on the passenger side. The driver side extensions can be shimmed and wedged from moving much easier than the passenger side. One screw up on that bolt head and you will be required to grind if off, or remove intake and probably grind anyway, or pull the engine out, or to make some other tool to grind the bolt off with. Remember to top off and burp and top off your cooling system after finishing if you removed the heater core hoses for access!!!
The top starter bolt is a pain, but can be easily accessed in from of the x brace engine mount with the right length extensions and a universal.
The bottom passenger side exhaust nut is 15mm. This requires the engine square, careful of broken mounts, a ½” drive 15” 6 point socket that is just deep enough, extensions, and ½" universal. Standard short or long sockets will bind and cause another big issue. Have this socket handy. If you don’t have the right length 15” socket and can’t get to the store to find one, cut a deep socket down. Once stuck due to using the wrong tool for the job you will be required to get the right socket and twist the studs off. Not on a lift? Expect 4 hours with a 5” breaker bar to break the bottom stud off. Once you have the exhaust out you can use a small 4” grinder, high speed steel drill bits and a hacksaw blade in hand and can cut a slot from the edge of the flange right to the bolt stud. Weld a socket extension to the end of the stud, wedge a screwdriver in the slot to help relieve some tightness, and back the stud out with a ratchet.
On reassembly, crazy glue the passenger side exhaust flange gasket to the top of the pipe and carefully put the pipe into place without knocking it loose.
When reinstalling the 5 speed, go to the front of the car and get a standard 16 oz wood hammer and push the engine backwards so the tail tilts down as far as it will go and wedged it there with the hammer. A good place is just to the left of the radiator on the frame and to the valve cover. It is very important that the engine is pointed down as much as possible at the rear or the input shaft of the 5 speed will hit the clutch springs.
Do not ever jack your car up on a hill where it is leaning sideways without seriously preventing it from sliding down hill at both front and rear wheels. If your can slide sideways jacking it up it WILL slide down hill as soon as the last wheel leaves the floor, maybe sooner!!! If your surface is flat enough the 5 speed will balance on the jack, but try to rotate. Not a big deal. If you are on a hill you will need to be strong enough to lift the 5 speed by suspending the rear with your knees and benching it in.
Jack the car up only as high as necessary. Too much room means having to life the 5 speed higher.
Make sure your oxygen sensor wiring is away from any exhaust pipe and secure them to insure they will not get burned.
Work safe. Wish you all well. Thanks for all the great tips and sharing.
Had to fix many typo's. I'm tired.