Ive never heard of any "transmission problems" on the svt besides the Clutch issue. If nothing, ill give the Getrag that its a pretty stout trans. It holds up to some pretty serious abuse.
As for parts. The SVT and normal Zetec models are very very similar, so in many cases, they share the same part. For the parts that are SVT specific, yes they are more expensive than a Zetec on the whole, however depending on where you shop, you can usually find some pretty decent prices.
The good news is that all of the major issues the SVT has are usually pretty cheap to replace if you do the work yourself. The thing I will say however is that SVTf's are attention whores. If you do not give them the attention and maintenance that they need, you are asking for a huge hit to the wallet. So make sure to keep things clean, and check out any issue that you see/feel/hear before it becomes a chain reaction.