your budget will never be enough.... welcome to owning a Jeep product
Otherwise known as a Bankruptcy starter kit.
I would google images of Jeep Commanders and print out things you like. Actually cut stuff out and build your Commander with pictures is one technique.
Wheels can be resurfaced/chromed/de-chromed/repainted... So look at anything that catches your eyes. I love getting stuff super cheap and nothing pretty is cheap.
You can buy a basic 2" lift for about $200 that will let you run a slightly bigger tire and give a nice lifted look really.
I would focus on spending some cash to get the transmission checked out and the fluid changed first off, do all the maintenance stuff no one ever really does until it is too late... Change the differential fluid.
Lower control arms have crappy rubber joints that many of us have had to switch out, so check those.
checking all that stuff will make lifting and modifying the Commander a much happier experience.
All the programmers work... some lean towards the Flashpack system or others go with Diablo brand stuff... Both work fine.
Before you buy anything, check the for sale forum and post what you are willing to buy and someone might have what you want. If I was not deployed I could send you extra lifting spacers I have lying around my garage. The Jeep community has folks with garages full of used stuff they do not use anymore because our Jeep addiction rivals crack cocaine when it comes to bigger lifts.
'06 Hemi Limited 4X4, 6(ish)" lift, 35" General Red Letter, 2" spacers, Mopar CAI, RER and mygig lockpick, blue Interior LEDs, stub antenna 3", Callahan Red Brake set, 6.1L SRT8 exaust headers, full custom 3" exhaust from headers back, Fastman 847 ported TB, BBK Fuel Rails, 6.1L injectors, JBA UCAs, Nitro gear 4:10, SA hidden front winch mount.