I think that updating to the latest dash after the XGD3 became official would put you at 13146. if i am correct. It may be 13599 that you're on actually. So, if am reading correctly, you didn't take an freeboot/modified nand update. That was probably your error. The stock dash would of negated some things that applied to the cygnos/freeboot days.
You needed to use a modern Freeboot toolbox utilitly or Xebuild or Multibuilder, Jrunner to take care of the differences since the cygnos days. I think the latest jtag style dashboards and GPU shader injection exploit works by modifying smc.bin. There was specific soldering points to redo in order to take advantage of that method.
It's best that you just start fresh and explore the boxxdr alternate TMS/TDI audio clamp transistor method. And, please don't update the dash anymore as you may have to do an RGH 2.0 procedure for future modded console that runs unsigned code.
Remember JTAG is only good on dashboards below 8955. But, as stated above ,you can get above 8955 on modified dashes to run newer games. but that requires use of specialized freeboot/Xebuild/multibuild/rgloader/ tools to automatically rebuild you a fresh modified dash to run unsigned code.
edit:But you also may have gotten 3RROD as well. Since you're console is an old phat. Because running a stock nand shouldn't be any problems. So, i don't know. I doubt the XGd3 game caused the 3RROD though. It's just coincindence.