subie i agree with the other guys, those prices are way too high. these shops are working on the basis that since we're all used to paying $1000 for a pfc plus $500 for a tune, people will blindly jump at paying $1000 because it's cheaper. of course that completely ignores the issue of exactly what you're getting for your money! a shop in silverwater was asking $1800 for a Chiptorque remap when Chiptorque themselves in Brisbane were asking only $500. go figure, i know what i call that.
if you send your ecu to Nistune they will install the new board and return it to you for $250. you don't get the software to tune yourself for that , you have to go to a tuner who has it. a single user licence that allows you to tune yourself costs an extra $200 from memory, but then a multi user licence that tuners buy allows them to tune as many cars as they want and only costs $600. you might like to ask some of these shops why they effectively want $750 for a tune when it's so similar to a PFC, i'd be interested to see their response.
as you correctly state that's all well and good, but that's what they're charging so what are the options? not sure if it's of help to you but i know that Autotech in Canberra have Nistune and will not charge you anywhere near $750 for a tune, more like $200 if it's straightforward. throw in $150 for fuel and your up for $600 or so total. also the Nistune website has a list of tuners, try there.