There's a few ways to do this;
1) You can get a UV EPROM eraser and burner, and burn your own, not the best way to go (old School). Some guys over in GearHeadEFI still have the capability to do this.
2) (better) You can solder in a 28 pin chip holder to accept the 27SF512 flash EEPROM. You'll need TunerPro RT v5x, and ALDL to USB cable, Moates Burn2 chip flasher, and, of course a laptop. In the XDF mask ($42-1227747-V5.9.3) there are hacks for EGR delete, Hyway Lean Cruise, and a patch so you can monitor your injector DC and Pulse rate. I did this for a while but the OE 1227747 ECM was too slow (160 baud rate) and the tables too small for higher revs.
3) (Best IMHO) Get the Dynamic EFI FlashII (for ~ $450) which runs at 8192 baud, has automatic VE tuning which will also tune WOT with a WBO2, can run boost and N2O. Has 8 "banks" so you can flash and store 8 different calibrations on it. It uses TunerPro RT for modifying your .bin and it's own proprietary WUD (What's Up Display) where you can monitor/troubleshoot your system as well as data log. Down the road, if you change anything on your engine, you can easily tune for it.
In all 3 options, TunerPro RT is the best tool