In order of importance...
Number one, a louder horn. It really can save your life. And by loud, I mean Walls of Jericho volume. There's more detail on how to make all these changes on Deti's transalp pages http://www.ta-deti.de/ta/

Improve front brake
This is the only necessary expensive modification. Pre '97 models have a single disk that is not really up to stopping a loaded bike quickly. At the very least put on a stainless steel cable. But it's best to put on a higher performance disk too. Unless you like sailing through red traffic lights with a rictus grin that is.

Metal Bash Plate
Make one if you can, or attach a plate of metal underneath. I have put on the centre piece off an early Africa Twin which can be easily adapted. Africa Queens offer a fabulous piece of kit with built-in tool boxes, but you'll have to sell a member of your family into slavery in order to afford it. Deti's site has suggestions.

Cover that headlight
They cost a lot of money those headlights, so get a perspex sheet, cut it to size, and drill appropriate holes in the the front faring for fixing. This modification is dead cheap and will do wonders for the uglyness of your bike.
Plate welded onto side-stand
Insecure surfaces abound where you're going and, given that bikes work better vertical, it's wise to get that weld.

Dump the plastic
Take off the side farings and leave them at home. They are only going to get broken on the road. If you must keep them, then get metal crash bars fitted.

Larger fuel tank
Most don't, and it's not really necessary, but, seeing as an early Africa Twin on fits straight on, it is a temptation. This will increase the weight though. This can turn into an expensive extra however, as the AT tank will require a fuel pump and fuel level sensor. Again, Africa Queens have a very nice, very costly, range of tanks for the TA.

Stiffer spring for rear suspension
Suspension is where the manufacturers' beancounters save the dosh for more important things like executive armchairs. The stock one is decidedly squidgy. Although some have managed with it, mine gave out somewhere on an Indian lunar surface misappropriately called a "road". A new spring is pretty cheap. If you want to splash out, a whole new unit from Technoflex or Ohlins (left) will transform the feel of the machine.

Sealed battery
It sure bubbles. The TA battery loses a lot of water through evaporation. Save yourself some bother.

Chain lubrication system
Good for the wet. Saves effort. But not necessary if you are religious with your chain oiling and this daily genuflection can only help the two of you grow closer.

Air filter
Drier than a camel's kaftan, and all that, dust will clog your air filter and maybe creep into places where it can do serious damage. The high quality K&N air filter for the early Africa Twin fits into the early TAs. They last for ever without cleaning and re-oiling, and they provide a touch more power, allegedly. Again, see Deti's site for information.

Spares to bring
The CDI units are the only things that can't be fixed up on the road. If you can afford these then take 'em along. Otherwise, a stripped down to the bones toolkit will contain 8, 10 and 12mm sockets and spanners, 17mm and 24mm ring spanners for the wheels, an adjustable spanner, a spark plug tool (very important as access is difficult), spare throttle and clutch cables, levers, inner tubes, puncture repair kit, tyre pressure gauge, multi-tool (Leatherman wave being the best) glues, WD40 and cable ties. Don't forget oil filters and, depending on the distance, tyres and chain set.

Packing
Everyone is different, but here are some thoughts.

First, pack light, of course. Three changes of underwear/shirt seems to be enough. Wash what you've worn on the road in the shower with you every day. You'll also need a warm fleece that fits under your riding jacket, and waterproofs. There are loads of packing lists on the web. We all bring too much with us, and then gradually dumpit along the way. It's part of the fun.

Artificial fabrics work. I would highly recommend Lowe Alpine dryflow T-shirts and shirts. As well as being breathable they are very easy to wash, and dry very quickly. I have been using them constantly for two years and they are still going strong. They don't look too bad either. Not cheap to buy, but they last and last. Similarly Rohan in London make a fantastic pair of trousers in super-strong super-light material. My Cargo pants have lasted two years being worn most days. After a wash they still look decent. They contain kevlar, and cost a packet. But cheap in the long run. They've withstood everything except an attack by a wild dog in Thailand.

On the feet a pair of riding boots that you can also walk in saves a lot of space. And most people go for this system along with a pair of sandals. My CAT boots took me around the Annapurna circuit and all the way to Australia in a lot of comfort. The protection level is very small though; and overlanders I know who have had serious accidents while I have been travelling have all hurt their lower legs badly. Thus I bought a pair of heavy tough motocross boots in Australia that I wear all the time. I carry some flip flops in my camelback and a pair of light trainers in the luggage. This works for me excellently.