Brakes are fine just did them...

 

I read that it was bad for the seals to flush high mileage transmissions. Also if the fluid is brown you want to gradually take it back to pink by doing multiple drain/fills and filter changes over a few week/month time span.

 

Same reason you don't so a flush on an engine. The big concern is dislodging debris and clogging oil galleries or getting into all the stupid little hydraulic bits in automatics. For a transmission or engine with unknown history, the proper and safe approach is to simply change the fluid frequently and let the detergents do the work. In XJs, only about half of the system's total fluid comes out when you empty the transmission, so when you perform a "drain and fill" you're changing the oil very slowly to avoid shocking anything and risking clogs. Which is good, because unfortunately it's far too common for some of these transmissions to see one oil change per decade.

 

Hang on there. Clutch packs in an automatic transmission are expected to wear over time. As soon as you let it shift, you've put clutch material in there. This is expected. Dark, burnt-smelling fluid (D/M turns dark when it's overheated, btw) is very bad to leave in as it no longer meets the lubricity, viscosity (remember, automatics are hydraulic) and additive requirements of the transmission. The ONLY reason to not change the fluid is if you know there's nothing left of the clutches and you need to get to the parts store for new stuff. The majority of slipping transmission faults are actually a result of bad fluid. So get that crap outta there!

 

My 2WD trans had darker than usual fluid.
As soon as I did a drain and fill it had issues and took a couple of seconds to enguage form park to reverse, reverse to drive ect.

Just speaking from my experience

OP sound slike you need to check the car over more then...
Get under the car and have somebody shift through the gears. See what moves more than usual