My suspicion is that you have one of two faults;
1) the gear adjustment is still wrong somehow; a sticky cassette joint or something will do it; or...
2) you've 'done something' to the hub innards during your oil bath.
In the latter instance if you have a drag spring hub (with castellated roller clutch retainer) failure to refit the drag spring correctly will produce a drive fault in gears 2-4 and 6-8. But the #1 fault I have encountered is that a ball comes displaced from the ball-ring when the hub is reassembled. It is
incredibly easy to do this, mainly because the design is a bit poor; a better design would go together more reliably.
What seems to happen is that a ball goes missing from the ball ring during reassembly. Most usually it gets as far as the nearest ratchet in the hub, which is right next to the ball-ring. Here, a ball will foul the primary gear train. This will generally produce a fault in either gears 1-4 or gears 5-8, and (in rare cases) both, depending on how the loose balls sit exactly.
The primary gear train in most 8s Nexuses (Nexii..?) has a clutch (C1) with four pawls which transmit the drive in gears 1-4 and are overrun in gears 5-8. These pawls engage two at a time; the other two do nothing. It is pot luck which pair engage. If one pawl engages and the other doesn't, the drive will slip. There are two springs (circular wire springs, looking like oversized snap rings) that both locate and spring the four pawls. Each spring springs two pawls and helps locate the other two. [Normally you can see one of the two springs in the gap between the driver and the R1 ring gear, right next to the ball ring, when the Centre is out of the hub.]
I have now seen several instances where a loose ball has fouled one of the pawls and deformed the nearest (visible) spring. This immediately results in foul noises and if the hub is ridden very far usually something breaks before too long.
To diagnose properly, remove the cassette joint, the sprocket, and the dust cover. Now look at the ball ring clip. Is it deformed? If so, don't panic, you can buy this part as a spare. Now look closer; are all the balls in the clip or are there any (even one) missing? If so, you need to pull the Centre, and find the missing ball. Often you will see the rogue ball sitting in one of the C1 pawl pockets.
Regardless of whether you can fish the ball out or not, you should really inspect the C1 clutch for damage. Only if there is clearly no deformation to the visible spring (and all four pawls are OK) could you take the risk and omit to do this; however normally you simply can't see well enough to be sure of this without further disassembly.
To inspect properly you need to remove the circlip on the left end of the Centre and remove the main planet gear assembly, which comes off in one big lump. [There are detailed instructions with photos on how to do this on the shimano.com website in the 'techtips' section, but it isn't too complicated]
I would suggest that you remove the C1 pawl springs one at a time (else all the pawls fall out) and check them (and the pawls) for damage. I'd suggest that you remove the pawls only one at a time too, so that you are sure they go back in the right place. Note that there are two types of C1 pawl and each similar pair must be installed 180 degrees apart, so that the nearest neighbours to each pawl are both of the alternative type. Deformed springs can normally be reset round, but broken pawls cannot be replaced; shimano don't sell these as spares...

. In an emergency it is OK to run with two pawls set 180 degrees apart, but both springs must be fitted; whilst only one actually springs a pawl pair, the other helps retain them too.
When reassembling the hub I have found that the ball ring is at very much reduced risk of damage if the Centre is rightside down when it is put back in the hubshell; this is the exact reverse way to the 'obvious' way to do it (lowering the Centre into the wheel set rightside up), but rightside down, the balls in the ball ring are at markedly reduced risk of getting displaced into the wrong spot. If you have a bench vice, you can clamp the Centre (less the dustcap) in it, left side upwards, and lower the wheel over it. Better still lift the loose centre into the wheel from below (i,e, whilst rightside down); this way you can be better sure you have not displaced one of the four pawls (on those Nexus versions which have them) on the left end of the Centre.
Once the left cone is installed (and adjusted finger tight to start with) you can check that the hub turns freely and that all the balls in the ball ring are present and correct. Once you are sure of this you can replace the RH seal/cover, the sprocket, the cassette etc.
It seems very boring and unnecessary to remove all the external gubbins from the Centre, but IME it is the only way to be absolutely sure that all the balls are in the right place.
BTW, for a lubricant, ATF has the virtues that it is oily, readily available, and pretty cheap to buy. It is however, not an especially good lubricant for slowly moving, highly loaded gear trains. Better than that is gear oil, and probably better again is (the right kind of) semi-fluid grease.
If you want an idea of how much worse ATF is as a lubricant, consider this; if you buy the most expensive ATF you can buy, (which is fully synthetic stuff costing about ten times as much per litre) the best that can be said of this magical elixir is that its lubrication properties are
as good as a standard hypoid gear oil. Standard ATF is quite a lot worse (as a lubricant) than gear oil.
hth
cheers