I don't think it'd be a good idea to run different injectors...they all flow differently. I would replace all 6 as well - if you have 3 bad here, you may have 1 more bad in two months, and the others go bad three months after that. It's better to take care of all of them at once. I understand what you mean, about doing right even if you are getting rid of the car soon, and I respect that a lot. Kudos.
If you don't feel comfortable doing the job, I wouldn't recommend you do it. If they aren't installed right, they can cause lots of problems, leaks, etc. There are a lot of guides and information on here and the rest of the internet, so that does help if you decide to DIY. You might also be able to find a another Z32-inclined mechanic or enthusiast locally to help you do the injectors at a much mroe affordable cost. Where are you from?
$1,100 seems a little high. A fair labor rate now-adays is what, $110/hr? That means 10 hours...pulling the intake plenum and changing injectors is no walk in the park, but I think 10 hours is stretching it, on the more expensive side.
For the injectors, I would order the parts from ImportPartsPro.com
You can get the upgraded old style injectors for under $1,000 (Nismo 555cc) (you would need to buy the fuel rail to plenum seals separately)
http://www.importpartspro.com/ni55inni30.html
Or go with the upgraded new style injectors, with the fuel rail conversion kit and all the seals you would need for $1,200(Nismo 740cc)
http://www.importpartspro.com/ni74inand300.html
If you go with the second option, (I am not 100% on this, somebody chime in here please) you might need to get the 300degree fuel line kit for $110 to complete the conversion to newer style injectors and upgraded fuel rail.
http://www.importpartspro.com/sz300deinkit.html
The second option is a better option all around - longer lasting injectors with more potential to support additional performance modifications the future owner might decide to install. It's also cheaper than the prices you were originally quoted anyways. Whatever you want to do, I would definitely get your parts yourself. Shops don't usually buy smart for you, if you want a good deal you probably have to find it yourself!
Hope that helps a little
