absolutely no issue with the different wall thickness. Aluminum has a heat transfer that is really good which means that you will get a uniform temperature. I would just make the soak times longer to give it time to get to temperature. No need to get slower, if anything you might go slightly faster as the big mass will slow things down.

Great thanks! I did pick up a few extra temp sensors.  maybe ill bore a couple holes in tbe thickest area of the mold to insert temp sensor and monitor

If you have the opportunity to do so this will give you some very valuable bits of information. just have a look at the time as well and make a graph over time to get a better feeling for the next time.

Like above, when very cold the prepreg wont stick well, what you could do is preheat your mould at around 25-30°C that way your prepreg will find an easier way to stick, or use a heatgun. 
Once your first ply is well against the mould all the rest should stick pretty well to each other. Ambient working temperatures are ideal between 20-25°C for prepreg lay up (at least that's what I think ) 

Sounds good. After watching a few more videos, it looks like +/-45 is great for getting into corners so that should work to my advantage. 
Couple more questions before I order prepreg. I'm still a bit unclear on whether or not it's an advantage to use single sided prepreg for first layer. I see that easy composites sells a prepreg that is optimized for the surface layer and it's single sided. I'm in the US so can't order their stuff, but should I pick a single sided for my first layer, or is it gonna make much difference? The part will not be getting clear coat or paint so I want it to come out of the mold with good finish. If 2 sided is not much of a disadvantage for surface layer, I'd rather use it since I need it for other areas. My other question is the bagging technique. Eventually I want to try a silicone plug if I go into production, but for prototyping I'm just gonna vacuum bag it. I'll make a tube out of bagging material that is slightly larger than the inside of my part.  This will be fed through the middle once mold is closed, then I'll bag the whole mold and seal the outside of the ends of that inner tube to the outer bag. Before closing the mold I will apply release film to the laminate, leaving a strip of laminate exposed for the overlap, then close mold and push overlaps down. Question is, do I need a breather between the release film and the bagging material? In most videos I watch, they use breather, but in the tutorial on this forum they bag straight onto the release film, only using breather on outside of mold. It will be much easier for me if I can do it the same way and only wrap breather around the outside. Will this work well in my case?