What was your process? Did you spray the cleaner on and simply rinse it off? Did you spray it on, allow to dwell then agitate with a brush before rinsing?
It may just be a case of not enough mechanical agitation, could be you need a stronger cleaner, could be both.
I've had great success using wheel acid on parts like that in the engine bay. There is a very important process in doing so though.
I spray the wheel acid on a totally cool, dry, pre-cleaned engine and above all I am very focused on keeping everything consistently wet with the wheel acid as I agitate with a brush after a minute or so of consistently wet dwell time.
So it's spray the wheel acid on, allowing a minute or two of dwell time while respraying if necessary to keep the cast aluminum parts thoroughly and evenly wet with the product the entire time this process is carried out. After the few minutes of dwell time I begin brushing the parts with a long and soft bristled brush being very careful not to splatter the wheel cleaner on myself or other areas of the car.
I am fully gloved up and using a respirator and most importantly eye protection while agitating (actually through the entire process start to finish) the parts in a fully and consistently wet manner. So it's spray (did I mention keeping everything consistently wet?) dwell, brush carefully while continuing to spray the wheel acid on the parts being cleaned in order to keep everything consistently wet.
Once everything has been cleaned sufficiently with the wheel acid, it is very important to rinse everything well with flowing water for at least 5 minutes as acid tends to permeate and cling to cast aluminum no matter how long you rinse it off. As such, you must follow this thorough rinsing with a alkaline based all purpose cleaner to penetrate and neutralize the acid that will naturally cling and permeate into the cast aluminum.
This neutralizing process is very important!! If not done, the aluminum will turn white as it dries because of the acid that will be left behind in the cast aluminum.
Keep in mind that you can also get this whitening effect if using a super strong concentrated alkaline cleaner such as Zep Industrial Ultra Concentrated Purple Degreaser.
I like to use Zep Citrus Degreaser cut 50/50 with water for this neutralizing procedure.
After the acid cleaning and thorough rinse, (while everything is still wet with water) I spray on the Zep Citrus and follow the same procedure as was outlined in the acid cleaning instructions above. That is, spray on thoroughly and allow a few minutes of consistently wet dwell time, brush agitate while keeping everything consistently wet by continuing to spray the Zep Citrus while agitating with the brush. In the end, I do a thorough water rinse then give the cast aluminum one last wash and rinse using a bucket of car wash & Wax concentrate mixed at regular car wash duty concentration. The wax in the wash & wax leaves behind a nice layer of protection against oxidation of the newly brightened cast aluminum.