Just set the nuts so all the slack is took up with minimal free play at the pushrod.
If it's that badly worn? Upgrade to the later setup with the over center spring TD5 on I think. Easier on the knee, think I paid £15 on eBay for the complete box/pedal/master but you don't need everything I believe.

I will keep an eye out for one. I have set it all up now but the bite point is at the top of the pedal now, I have slight play at the push rod, the trunnion is positioned further towards the end of the rod, moving the trunnion further along the rod towards the master won't move the bite point towards the floor will it?

nobber said:

I will keep an eye out for one. I have set it all up now but the bite point is at the top of the pedal now, I have slight play at the push rod, the trunnion is positioned further towards the end of the rod, moving the trunnion further along the rod towards the master won't move the bite point towards the floor will it?

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it should do ,adjust it back a little till bite point isnt as high

But with play surely the rod is fully extended?

It is yes. It's not a switch, clutch is released/engaged somewhere along the pushrod travel.
Do as @jamesmartin says, increase pushrod free play until it's how you like it. As long as there is free play there is no pressure on the thrust bearing thus no unnecessary wear or clutch slip in the extreme. Too much pushrod clearance is your original issue, now you've probably too little, that's not going to do any harm as long as you have some play. Somewhere between the two settings will feel right for you.
If you had someone to fiddle with your nuts whilst you stayed in the truck working the pedal it should only take a few minutes, on your own 1/2 hr maybe.