I have more less done the same trip but in two separate holidays; Egypt the first time and Jordan the second time around; not with GAP though. I have travelled with GAP on trips to other countries and they are very efficient and lead good tours.
You more or less have the highlights of both countries covered. I see that Abu Simbel is optional; definitely well worth a visit (my highlight of the Egypt trip).
On the Red Sea, some snorkelling is a must; of course if you are a qualified SCUBA diver then you should do some. If you are not qualified, most dive centres allow you to do a "Try Dive" if you want to give it a go.
The only danger is that it is a lot to cram in two weeks; the Jordan portion is more easy going but unless you have a indepth love of Ancient Egyptian history, you are more than likley going to be "templed out" by the end of the first week. It is good that you are heading to the Red Sea for a couple of days as this will give you a break.
I prefered Jordan much more than Egypt; Wadi Rum and Petra are spectacular and floating in the Dead Sea is an amazing experience.
September is a good time to go but be aware that it still can get quite hot; plenty of sun cream, t-shirts & shorts; can get a little chilly at night in the desert so does no harm to bring a lightweight fleece; almost never rains so no need for rain gear.
Healthwise, don't bring Immodium with you; buy some of the local stuff in a pharmacy as it works far better "local drugs for local bugs"; hopefully you won't need it but at least 25-30% of people get some illness especially in Egypt; just take the normal precuations; e.g. no ice in drinks, drink only bottled water, try to avoid salads. Also you should ensure that your travel vaccinations are up to date; Hepatitis A and Typhoid at a minimum.
Visas are obtainable at border & airports and can be usually paid for in Euros so no need to buy in advance. As for money just bring your credit card and withdraw from ATMs; no need to buy money in advance.
In Egypt you will have a lot of hassle on the streets no matter where you go with people trying to sell you their wares; just go with the flow. Beware in the markets for pickpockets; haggle for everything; some sellers start off at outrageous prices so don't feel bad about starting from very low. In Jordan, I was pleasantly surprised to have no hassle on the streets; in fact the only place where there was anybody trying to sell things was Petra.
As for alcohol, unlike places like Saudi Arabia and Iran there are no worries in Egypt or Jordan, plenty available