My truck is an early CR, it had the fuel filter canister mounted oem lift pump, so yes, it was removed. Glacier Diesel Power supplied me with an adapter to replace the oem pump so I could continue to utilize the factory canister/heater/filter, along with all the necessary hardware, relay, fittings, bypass Y, everything I needed to complete the modification.
I used all Parker Push-Loc fittings and Parker 3/8" rubber Pusk-Loc fuel line, they are top of the line and do not leak, and do not need a hose clamp to secure. I do carry a spare pump, 6' of fuel line and a few Parker Push-Loc barbed fittings under my back seat, the spare line is because once the line is correctly installed onto the barbed fitting, the only way it is coming off is to cut it off.
I spliced into my existing metal fuel line in front of the fuel tank, installed my new filtration, then the new pump, by-pass Y, and the rest of the necessary lines to complete the install. You could call Richard at Glacier for any advice on your truck, he is very helpful and will save you any possible headaches that you may encounter with the mod you are attempting. He no longer sells Walbro, but still recommended one to me for ease of future changeout.