That background helps.
I think you are fighting three issues and now introduced a potential 4th.
1) It appears your timing is off. I would start by timing it. You can search articles on this site with the key word “tech time“ a brand of meter you can find on eBay for about $200. Most diesel shops do not have one or one that still works. Setting “By ear” only gets you close.
2) It sounds like you have a fuel issue (Bucking), being a new truck to you it could be a few things. You said you replaced the fuel filter so you can skip that.
a) You turned up your pump all the way which could be overwhelming a week fuel delivery system. Also may add to smoke issue when starting. You should replace injectors and pump together. Your pump is likely out of time and now you have maxed it out. So probably time to have it rebuilt and set correctly.
b) You should replace your fuel return lines, caps and o-rings. (Most do so with the injectors.) If you did not likely a big part of your fuel issues. These are very common the first place to look for a hard start and smoke at start. Generally the o-rings fail or the lines crack both letting the system loose prime and drain off to the tank. Thus causing a hard start.
c) You should check your fuel delivery lines (From tanks to IP) for diesel leaks that have collected dirt. I would also if in the budget replace the mechanical lift pump and rubber hose to it. This is a common point of failure and often hard to diagnose when starting to fail. Many have used a 5 gallon gas can with diesel, an electric pump, and hooked to the line going into the fuel filter. Test drove to see if the issues went away. Confirming the fuel delivery is the issue. If the PO switched to a electric lift pump, search on those. Some have had a good experience, many found theirs ran out head room at high rpm. I personally like the mechanical pump, simple and works at all rpms.
d) The tank selector valve and the fuel tank pick up lines are also problematic. The tank selector valves are old and common to failing while between tanks causing drivability issues. The pick up ends called a shower head come loose and fall off. Then the tank only goes to say 1/8 tank and sucks air as the gas swishes around.
3) It also appears you have a glow plug issue. Hard starts and smoke till you warm up.(Being out of time also causes smoke fyi.) Complicating your issue is 87‘ was the change over year from the early 6.9 gp system to the 88’ 7.3 glow plug system.(Some report their late 6.9 model has the new style gp controller.) They are very different and used different wiring. You can get a new system to work on a older truck but you will have to do a little wiring. It also is an option to install a momentary push button connected to ground to turn on the glow plugs on either system. So send us some pics of your current glow plug system and wiring. Then we can tell you what you have and how it works. In the meantime check the glow plugs with a ohm meter. Unplug the glow plug electrical connector and test the tip with one probe of the meter with the other tip touching a good ground. You should see resistance. No resistance or a ”open” is a dead glow plug. Only buy Motorcraft glow plugs, others report off brands balloon and get stuck or break off in the head.
You have several items needing to be addressed, but once you do your truck should run much better and consistent.
