Took a bolt out of top of gearbox thinking it was

Repair your vehicle right away. Just click on the link I attach 2003 2008 Holden Isuzu Rodeo Ra TFR TFS Repair Service Manual Download

i would think the selector linkage internally are misaligned , have to remove gearbox and have it opened and inspected

your diesel engine should have a center bolt holding fuel filter it in place.you place drain pan under fuel filter when you remove top center bolt while holding fuel filter then remove old fuel filter then take new fuel filter add few ounces clean diesel fuel in new fuel filter lubricate gasket new fuel filter cartridge then install new filter crank engine check for leaks.

if a manual gearbox then check the oil level in the gearbox ,it has to ba newer model because the old minis used the engine oil in the gearbox as it was all in one

This information is from my genuine service manual. I hope it is of help.
Non-turbo
Turbo
Sedan Wagon
Type 5-forward speeds with synchromesh and 1-reverse
Transmission gear ratio
1st 3.454 3.454
2nd 2.062 1.947
3rd 1.448 1.366
4th 1.088 0.972
5th 0.780 0.738
Reverse 3.333
Front reduction gear Final
Type of gear Hypoid
Gear ratio 4.111 3.900
Rear reduction gear
Transfer
Type of gear Helical
Gear ratio 1.000 1.100
Final
Type of gear Hypoid
Gear ratio 4.111 3.900 3.545
Front differential Type and number of gear Straight bevel gear (Bevel pinion: 2, Bevel gear: 2)
Center differential Type and number of gear
Straight bevel gear
(Bevel pinion: 2, Bevel gear: 2 and viscous coupling)
Transmission gear oil GL-5
Transmission gear oil capacity 3.5 2 (3.7 US qt, 3.1 Imp qt)

wierd not normal. are you sure you have eased off the throttle enough just before you dip the clutch, diesels can lag slightly, is it a turbo? turbo could create even greater lag

i can't change into 2nd,4th and reverse gears. i think its a gear lever cable not sure doe any ideas?

im not telling you what to do because it could be a bad transmission and an easy fix but I cant tell without looking at it , but if its a hard fix just go to a reliable junkyard and get another

if its a manual then you have moved the splined shaft under the car ,just re adjust it ,slacken pinch bolt and look for original marks in the grime to re set it

you need to have the throttle body cleaned out or replaced