We had a slightly different experience from above, so thought I’d add some info.
It’s true that all the paperwork is fairly easy to get done yourself if you have a couple of days (certainly don’t stress about it in advance), but by far the most difficult part of the process is getting a space for your car on a barge (bikes easier I think). To do this, I would recommend ringing up at least 3 weeks in advance. Barges are sporadic, with no fixed timetable or capacity, so you’re mostly getting yourself on the priority list for any spaces that do appear.
The fixers can do this for you, but if you want to be ‘belt and braces’, the guy who the fixers call, who manages this list is called Mahmoud Baraca (Tel 012 82539341). He’ll need the name of the car owner, your port of entry, and your Egyptian plate number (it should be punched into the plates if you look carefully, and they might tell you when you enter)
He’s really nice and speaks decent English. If you do call up and say you’re coming though, do try to turn up on time, otherwise everyone gets very annoyed and you might get bumped down the list a bit.
We managed without a fixer, doing most of the paperwork ourselves, but it was only with significant help from Mahmoud that we got on the barge because the barge captains can be such tricky so and so’s! (other travellers were similarly reliant on their fixers)
Once you are on the car barge, you are guaranteed a ticket on the ferry, so no need to stress about that in advance, but befriending Mr Salah does increase your chances of getting a cabin, so worth it if you have time.
We met all the fixers, and to add to previous debate (we were certainly confused before getting to Aswan), I would definitely use Kamal. His English isn’t great, but definitely sufficient to get the job done, and he’s a decent guy (heading south, he usually just asks people to pay what they think it’s worth). Abouda will get the job done for you too, but you’ll over pay for everything, and although he was perfectly pleasant to our faces, we heard numerous stories of him turning nasty when things went wrong (which they often do in Aswan).
The big thing on fixers though, is to get better value from using them for everything you can for the same fee (ie sorting petrol, rides back and forth to the port, changing money, etc)

Finally on Aswan, if you have any problems / questions at all, you can ring Mohammed at the Adam Home campsite (012 2442167). He speaks good English, is completely independent of it all, and will look after you (though probably don’t listen to him when he tells you don’t need a fixer!) Adam Home is a great place to meet overlanders, and genuinely has hot showers (as well as amazing hosts).
A few quick tips for the ferry / Sudan:
• You can sleep in front of the captain (for a small tip) on deck with plenty of room to lie down (turn left when you enter the boat, past all the first class cabins on to the front deck, and then up the ladder)
• It’s bloody cold at the moment, so take a sleeping bag and lots of warm clothes (make sure to take all this out of your car before you board the barge, it can be difficult once on board)
• Use Mazar as a fixer when you get to the other side, a really nice guy who will look after you (+249 12238070740) – if you ring in advance he can book you the nice Cagen hotel (80 Sudanese per night for a double) – there can be issues getting rooms when the ferry is in town (mostly locals waiting to catch the ferry north)
• Bring all the cash you need from Egypt – no ATMs / bank withdrawls anywhere in Sudan
• The road is now tarred all the way to Ethiopia – Khartoum is possible in 2 days, by taking the new bridge at Dongola, but there is also good tar across to Karima and Atbara if you want to see a few more pyramids (though the last couple of hours into Khartoum isn’t much fun, since you pick up the truck filled road from Port Sudan)
• In Khartoum, National Camping (N15.52483 E32.57042) is much nicer than Blue Nile, with warmish showers

A small tip if you put your motorbike on a barge from Aswan to Wadi Halfa (or the other way as well i guess).
Make sure you put the bike next to the barge's bridge (captains place) where it is not surrounded with all the other cargo, so you can easily get it out.
We put our bike next to the barge's fence (and tied it for it) but then guys loaded the barge with looooads of cargo, so once the barge arrived to Wadi Halfa (2 days after us), we had to wait additional 2 days untill they unload everything else out of the barge so that we can get our bike out.
Cheers!