Problems continue and don't know what to do

[JAZZCNC]

I think I might have an idea concerning the jog movements. I set frequency at 35000khz in ports n pins page, again, just following the set up, but I woke up this morning and thought I should change it back to 25000khz.

So I'll try that when I get in from work.

Don't mess around with the Kernal frequency going higher than 25K will only stress out the parallel port and cause other troubles.

You need to take things one step at a time and break the process into little steps. Mach3 won't do anything if the I/O pins are not set correctly so this is the first place to start.
Start with Safety first and wire in the E-stop if it has one. Find the pins it's connected to and enter pin # in E-stop Input.

Then start with getting movement, one axis at a time. Which by the sounds you have the correct pins set because got movement.

The next step is tuning them to move correctly in Motor tuning. The first setting to deal with is "Steps per". This will make it so moves the correct amount. The easiest way is to See the link Clive posted with my reply in another thread.
The second step is Acceleration and Velocity, Start with low numbers at first and slowly increase one at a time, never both together, and test until the motors Stall. Then back off 25%. If these numbers are too high the Motors will stall(whizzing/humming sound)
Good start numbers are (If using metric units) Velocity 500 Accel 250. Even the crappiest machines should reach those speeds without stalling motors.
Leave the Step pulse and Dir pulse = 0 unless you get erratic behavior.

From here it's up to you where to move onto next. But whichever you choose only ever work on one thing at a time until it works as you expect or desire.
Just remember that if the Pin # are not set correctly for Input or Output Mach3 won't know anything about it, so even if wired correctly on machine Mach will be oblivious to it.