Regardless of the order, slightly heavier oil did not cause the rod knock. I would suspect some other issue, for example the oil level was too low and caused the pump to go dry, the shop monkey forgetting to put the oil filter or drain plug back on before starting, or the introduction of contaminents during the oil change. Heavier oil generally provides better protection for the bearings because it allows for a thicker film layer. It isn't as if the engine was filled with 75W-140 rear end grease.
If it really is a bearing noise, then you obviously have a limited number of options and have to choose based on your budget and mechanical ability/experience:
1. fix it yourself. Don't attempt unless you have experience and be sure to do a full rebuild, new rings, seals and bearings. Have a machine shop do the work you can't (like boring, honing or polishing/turning the crank)
2. Take it somewhere to have a new or rebuilt engine installed for you. If you haven't pulled an engine before, this probably isn't a good time to learn, so let a professional do it.
3. Buy a rebuilt short block or complete engine and install yourself. Again, don't get in over your head if you aren't mechanically inclined.
4. Buy a J-yard engine (complete or just the short block) and install yourself. This is very economical and with some labor, you could get it done for just a few hundred dollars. The 4.6 is a strong engine that can live for 3-400k miles if maintained well.
I am more mechanically inclined, so personally I would buy a j-yard engine, get the car running and sell it. After sitting for 6 years, I'm willing to bet there are rear end seals and bearings, along with transmission seals are dry and ready to fail, not to mention issues with the fuel system from sitting!
Regardless of what you choose, make sure all the bearings and seals get replaced. If it wiped out one bearing, chances are the other bearings aren't pretty!