I have both a 96 X-90 and a 95 Tracker 2 door that I have recently removed the carpet from and am getting ready to apply the liner myself after getting a quote for $400 to do X-90 and install some boat drain plugs.  My questions are:

• Before I experiment where is the best place to locate the plugs so I can access them easily, want to be able to drain on the trail as well as when cleaning.
• What liner brand installs the easiest?  Roll-on vs. Spray? I was hoping for something other than black as I am in Florida and X-90 has glass T-Tops so it is already an oven inside.
• I know you need to scuff all the paint and I plan in reusing the plastic door sills to hide the factory wiring harness as I still have all my factory seat belts installed.

I do not know about the X90, but the 95 Tracker has the floor drain plugs already.

I would not use Herculiner ever again.  It wears real easy, and mine was course enough that dirt was always sticking in between the grit.
Duplicolor spray is better than NAPA.  It also comes in colors.
Duplicolor also comes in cans for spraying or rolling (I haven't used it yet).

X2 on NOT using Herculiner.  It is a pain.  The only thing Herculiner has worked well on (for me) is my brush guard.  I didn't shake it/stir it up to avoid suspending the rubber particles, I just dabbed my brush into the liquid at the top of the can and applied three coats to my brush guard... then after it dried, I sprayed three coats of Rustoleum semi-gloss black on it TO protect the Herculiner coating from the UV rays which breaks it down really fast.  It's now been over five years and there still isn't a spot of rust on the brushguard.  Mostly due to the Rustoleum paint, I think.

Monsta Liner supposedly has a good product that is UV resistant and holds its color well.  That's what I intend to use for coating Buster instead of painting him.