Can I make progress with bodyweight only?
For a long while, yes, by changing leverage rather than adding weight: elevate the feet, slow the eccentric, move toward single-limb versions. Progress stalls eventually on pulling movements, which is where something to hang from becomes the one purchase worth making.
How do I start running again after two years off?
Cap it by time, not distance, and keep the first three weeks conversational. Injury on a return almost always comes from pace, not volume, and the tissues that need adapting take longer than the fitness that returns first.
How do I know when it stops being worth it?
When you stop noticing it. If it has not surfaced a problem in six months, it is either solved or it was never the bottleneck you thought.