get the XR6 - the head flows better meaning that you wont need to port it unless you are really serious about more hp, and they have 3.45LSDs already :D
do you have insurance and want to keep it? if not then an aftermarket computer is the way to go, if you are planning on 'proper' engine mods ie porting, really
big cam etc.
firstly, as above, get an exhaust - probably hurricane extractors are the cheapest/best option, then a single 2.5" mandrel bent exhaust with a couple of straight through mufflers, and a modified cat, should be maybe 800 or so, depending on what you can get all the stuff for.
then get a computer (chips are ok but full aftermarket is the way to go), check out http://www.icenet.com.au/~pie
there is a guy in perth that modifies V8 computers to run the 6s, that way you get full programmability, MAF sensor and sequential fuel injection as well - though its about $2k for one of those, but depending on where you can find parts and what level of TwEECer you want it can be cheaper than that.
so you have a little over 1k left.
get a reground cam (dont regrind the XR cam ,sell it to someone on the forums!) give them a EA cam or something, and get a vernier cam gear, stiffer valvesprings, hardened retainers and collets. that last bit should set you back $600 or thereabouts, and depending on how big you want the cam you might need bigger injectors too.
make some kind of cold air intake with a K&N filter too - get the K&N from supercheap when they have a sale and it shouldnt cost more than $100 for the CAI and filter.
so you have about over $500 left over, you might be able to get a higher 'stall' stall converter from the trader or something i dunno.
then there is still a thermofan conversion, maybe shorter diff gears (3.7?) head work..the skys the limit!