Its not impossible that your fuel is that bad, but it is unlikely the real problem. Realistically, it is amazing you've never had any air in fuel problems up until now with the stock system. Most people who own a CRD make a lift pump priority #1 (#2 if the timing belt is due
) to eliminate problems like yours. If you prime the fuel filter head until you get nothing but steady fuel coming out, run it for 10 or so miles, then prime it again and get any air...that is likely your problem. If you have the first generation fuel filter head (the one WITHOUT the blue connector on the front is the OLD one) then it may have finally cracked at the heater plug like many have done. Yours just may have taken longer than other peoples to do so. You could have also had a seal fail in one of the flexible lines near the fuel tank that is letting air in. I suggest making this a high priority, even if it doesn't immediately fix the problem you're having. It is worth every penny when you consider the positive effect it has on the entire fuel system. Now, if the "limp mode" you experienced happened after the vehicle started to warm up or was completely warmed up according to the temp gauge, it is also possible you have a failing crank position sensor. It is a fairly inexpensive and easy thing to change, though it requires some contortionist abilities if you don't have a partner to help. I'm 6'2" and was able to fairly easily change mine out by myself from underneath in about an hour. I could do it in half the time now that I've done it once.
The crank position sensor would be the quicker and easier thing to try, but I still cant recommend a lift pump enough. There are guides here on the forum that can walk you through either procedure. If you can handle basic tools and maybe some simple wiring, you can handle doing either one of those repairs/modifications.