What I did with my tub was to send it off to the sand blaster. It cost me nearly 500.00 for that. Removing the bed liner is not going to be an easy job! Ask around or do a search about how to do this. Brake fluid might make it peel easily if its a cheap liner. I would remove the bed liner before you send it off to the blaster since most places charge for time and materials. Blasting that liner could be really tough. After my tub came back from the blaster I sprayed a thin coat of epoxy primer to stop flash rusting on the bare metal while I was working on it. I then went to town and started replacing panels. Of course brace everything before you remove panels. Just weld in some angle iron around the rear tailgate and around the door openings. If I had to do this over again I would do a few things differently.
1. I would do all my panel replacement and welding before I sent it off to the blaster. This allows you to not worry about flash rust or greasy fingerprints on your tub. Also sandblasting the welds makes it real nice and clean before you spray it with primer. The results are that you get your tub back nice and clean and ready to prime with an epoxy primer. Just clean it first with a metal prep to remove all the dust from sand blasting. I gave it a good wash with the air gun first then cleaned it with metal prep and then tac cloth. This results in the cleanest possible surface to spray your epoxy primer on.
2. I tried to take some short cuts by not removing the brackets in the wheel wells. The wheel well supports as well as the brackets for the captured nuts for the jump seats as well as any roll cage brackets. There is massive rust under those. I later removed them and boy am I glad I did. Remember to use your pot blaster to clean any seams after you remove a panel. For example: between the rear quarters and the wheel wells there will be rust. Blast it and prime it with a weld thru primer.
3. Pin holes in panels and on the floors. There is a product that you can buy from eastwood or probably sold at welders supply. A copper spoon will help you fill these holes . There is also a a kit from east wood :
Butt Weld Clamps & Backers Kit - Welding Clamps & Accessories - Eastwood
I think this kit would make welding sheet metal a hell of a lot easier. when you cut out a panel the remaining lip tends to bend in slightly and these clamps will keep the panels even and make better welds with less grinding. The copper backing plate will help with the burn through.
4. Consider Time V.S. Money: I have a lot of time and about 1200.00 in panels into my tub not to mention a bunch of money in paint, supplies, filler,tools etc. Probably at least 2000.00 plus 500.00 for sand blasting. As for how much time? Hard to say, but it took me 6 months to finish it. I did take a 3 month break. So at least 3 months of working on it 2 to 3 days a week with no help.

So a new tub would be at least 6000.00 if you went with a steel tub for a price comparison. Since your rig isn't a purist dream

I would consider an Aluminum tub. You would be better off with time and money in the long run. I would spend my time picking up some extra work /shifts on the side if your job allows to help save. That's just me and my Rig is more of a stock rig with a few exceptions.. That's why I chose to restore the tub. However the condition of your tub will be a major consideration of what to do. If its not bad then try to restore it. Oh and one more thing to consider when you look at my time frame is that I had to teach myself how to weld while doing this. So it might be a lot less of a challenge for you.

Brian