You can find a lot on how to do this and take a 2009 4,1 and DIY to 5,1 and cpu.
You can buy a 4,1 for $495 on ebay or Craigslist to start with.
http://forums.macrumors.com/forumdisplay.php?f=1
Your title is a little misleading. If they applied thermal paste and all, and have proper daughter card you will be fine like assembling or redoing cpu upgrades which are done all the time, and sometimes even the best experienced can bend a pin or have a learning experience 😉
The price on X5690 are good but you can usually get close but for a lot less using X5680 or even dual 4-core 3.2GHz - all depends and not everyone or everything needs or benefits from 12-core (heat, watts, and other concerns too). Often a 6-core 3.4GHz is the perfect sweet spot. If you need more than 48GB of memory then dual socket is called for.
The 4,1 will always 'suffer' some from sharing bandwidth in slots 3&4 and limit some controllers. And 5,1 firmware doesn't change the hardware in that regard.
An Apple/Samsung blade SSD of 1200MB/sec like the XP941 can boost performance, and then there are all the graphic video card toys to play with. Dual GPU, or even drive a 5k display (which the nMP 6,1 cannot do).
These cMP (Classic Mac Pro) models are popular and holding their own and being bought by enthusiasts.