I'm still at a loss about the stench you report; rotten-egg smell is certainly not unheard of though. There is a reason why most of us do these things outside, in a shed or in some other well-ventilated area...
I'm also pretty pretty sure anyone possibly living with you wouldn't appreciate any fermenting pineapple juice with fungus floating on top.
Having said that, keris Jawa blades can be especially porous and whatever happens to hide inside those crevices may differ quite a bit and possibly contribute to unexpected "features" as well.
The general rule for traditional/historic iron/steel: the greater the amount of carbon, the more susceptible they are to corrosion (i.e. rusting away). If any given steel alloy has been hardened, it corrodes even quicker than unhardened. For more details you can consult metallurgical text books but as Alan notes, this is not really needed for basic cleaning efforts.
Any smooth-looking edges with enough patina on them so that you can't see the bare steel anymore is likely to have patches consisting of rust rather than steel. When you start cleaning, the rust will fall off and these patches will look like in the pics you show (or worse). For keris Jawa this appearance is culturally accepted nowadays.
Regarding the aesthetics of the final result, I suggest that you're still in the middle of the cleaning phase: It would be good to proceed to remove all rust as Jean already suggested. One usually tries to limit exposure of the blade to any acid and manually scrubbing the blade and individually picking the remaining spots of rust as described by Alan really helps the acid to finish its job quicker.
Once the rust is completely removed (pics with flash can help to detect any remaining rust), you could try to rub a cut lime fruit over the dark areas, if you prefer lesser contrast. I usually do this as a preparation before progressing to warangan.
For pretty much any keris Jawa or keris Bali/Lombok warangan is needed as a final step to bring out the traditional look of the pamor. If you can't do that, it might be worth a try with other etching approaches including the cold blue suggested by Alan. While the exposed steel core will always stay visible (perfectly ok), the main part of the blade should have some pamor to show which would lessen the current B&W contrast.
The exact same thing happened to a moro kris I attempted to clean with diluted vinegar, and it turned out to ruin that moro kris in the end.
BTW, that Moro kris is far from ruined! (Unless you haven't shown us his most recent reincarnation...)
As far as I could see, the overall surface wasn't even porous and just needs "a little" touching up with some polishing effort. Needs a bit of tedious work but feasible even for any beginner.
The more experience one gains with restoration, the better one is able to predict the final outcome and the hopefully best strategy to achieve it with the least effort. Most errors or results of less suitable approaches do not tend to have severe consequences and can be remedied with additional efforts. However, it helps to obtain frequent feedback during each project to progress along the learning curve - I'd posit posting pics of the current status of any ongoing projects more frequently!
The more a blade approaches any relict/excavated condition, the more careful one should consider just leaving it alone though. (There is a reason why we tend to speak of "ghost" blades in forum parlor, especially with keris Jawa.)