New engine noises!

Right, turns out I'm a muppet. It is the clutch. When I press the clutch pedal down, both the whirring noise and the knocking noise disappear. Any likely suspects for this? On the up side, at least the engine isn't knocking!! Cheers.

The main suspects will be the clutch release bearing (whirring) and clutch release arm, onto which the bearing fits, so this and bearing for knocking. You tend to get the bearing with a clutch kit, was it replaced?
it's possible you will feel the knock on the release arm at the point the clutch cable is connected, but it may need an engine / gearbox split again to figure it out. If you paid someone for the clutch fit time to take it back.

The clutch release bearing if properly installed and adjusted will not be noisy with the clutch released and quiet depressed - the bearing sits over the gearbox input shaft and rotates only when the clutch pedal is depressed forcing into contact with the clutch cover.

A whirring noise that stops when the clutch is depressed is more likely to be a gearbox related issue - and if the problem was not there before the clutch was replaced, then whoever replaced the clutch did not do the job properly.

It has been in twice, and I'm reluctant to go back a third time! Clutch kit was fitted at same time as older type gearbox, so not sure if where the issue lays. However, when I first picked it up, there was no noise but the clutch slipped. Second time it was collected, clutch worked fine, but after a few miles the noise started (I did not notice any noise when collected?) Cheers

Ok, that's made things interesting. It's possible it's any of the above, even a gearbox issue if you don't know it's history.
Unless you take it back it's a DIY job, but start simple, look at the clutch release arm and feel for the knocking.
If you don't have the confidence then it's time to "phone a friend" and get some support on what you are experiencing.
Are you local to any other Jimny owners, maybe they can take a look.
I'm in Staffordshire and would take a look, but it's a location based thing.
Good luck.
M

Drive from the engine through the clutch and into the g/box via input shaft (first motion shaft) and then into layshaft (second motion shaft). This is as far as it can go without car moving, so noise is either:-
Input shaft bearing or gear to layshaft or layshaft bearing nearest clutch.

Roger