No start Battery good, will start when jumped to hotwire, replaced neutral switch, relay, and ignition

you stated pump kicks on put clutch in and no start so what would you hot wire [[and dont hotwire anything ]]]which causes more problems and in this case is probably pump not problem ----theirs a clutch safety to start in manual trans which that or ignition system problem such as failed starter --ignition switch --etc have vehicle for any possible trouble codes

Probably should check to see if there is power going down threw the small wire on the starter solenoid when the key is turned to the start position, that be a good place to start. Double check the battery cables, make sure they are in good shape, clean and tight. If there is no power to the small wire on the starter solenoid, it may be the starter relay, or even an ignition switch.

Is the anti-theft light lit ? Is the starter relay good ? Do you know what a relay is ? Are the battery cables good ? I would start will the starter relay circuit's if the anti-theft light is not lit.! The starter relay along with the starter relay diode is located in the battery junction box in the engine compartment. The relay is K-22 . If you pull out the relay an look on the bottom of the relay you should see four sets of numbers 30,87 an 85 ,86 . If you take a jumper wire (12-14 gage ) an jump pins 30 an 87 if the battery cables & connections are good the starter will crank . Pin's 85 &86 are the control side of the relay . One of these comes from the ignition switch when is start position an the other goes through the transmission range sensor (park neutral switch) To ground or the PCM if yours has a V-8 . Now if when you jump pins 30 & 87 an nothing happens you have bad connections or the battery cable is bad . You can go on youtube an check out videos on voltage drop testing the starter circuit .

if you have battery power on the large terminal at the starter and the same on the smaller wire when someone Is turning the key to start and the starter has a good ground then the starter is bad drawing too much amperage causing the clicking sound.

Yes there is a starter relay in the wiring diagram.
The yellow and lite blue wire goes from the starter solenoid to the relay. There is a yellow wire from the relay to a 30amp fuse. The key switch powers thru the neutral safety switch and then powers the relay on.

Here are some possible reasons:

Park/neutral switch is open.
Poor ground connection to starter.

You can test the park/neutral switch by either jumping the solenoid (connect the hot terminal to the start terminal to see if the starter cranks--if it does, the ground is good) or by interrogating the starter relay socket. To interrogate the relay socket, use a 12 volt test light connection the clip to battery positive. Probe the socket terminals with the test light. If only one terminal lights the light, your park/neutral switch is bad or the start wire to the solenoid is bad.

If it starts by jumping the starter you have a faulty electrical ignition switch

Could be ignition switch, battery/battery connection, starter, starter solenoid, or starter relay. (phew!) Remove your battery cables and clean the posts and terminals. (There's a really cheap and easy-to-use tool for this that works VERY well. Cheap as in 1-2 bucks.) Get your battery checked, too. Just in case. If you're pretty good with stuff like this, remove the ignition switch and hotwire it. If it starts every time, it's your switch. If not that, replace your starter relay. Cheap and easy. If not that, Get your starter/starter solenoid checked at a parts store for FREE. (You'll have to remove it, but most can DIY.) Good Luck.

Ford loves that relay.. Jump the two big posts on the relay. the starter should crank. the little post is from your ignition switch. Jumping the two large terminal bypasses the relay. Make sure the vehicle is in neutral with the brake set.Once you know how to do that, try to key dtart in park, then neutral. If it won't do anything, Your neutral safety switch is defective.
If it will start in any gears, again bad neutral switch. Be careful and good luck. Use a jumper cable to jump the two posts. Anything smaller can get you shock or burned.

It could be the ignition switch, neutral safety switch,alternator, ignition/starter relay, ignition coil/module.