To my taste, MIM weak spots are the frets, nuts, and hardware, especially the bridges – generally speaking.
Fixing playability and setup comes before parts swaps IMO. My first mods would be a new nut (or a fine tuning of the stock nut if possible), and a fret dressing, with a specific focus on smoothing and rounding the fret edges and slightly softening the fretboard edges.
I'd give the stock hardware a chance, and hold off on any swaps until the next string change – if the stock hardware felt lacking. It might do just fine as long as it is adjusted well and kept in good condition.
With a versatile enough amp, the pickup is usually fine IMO, but that could be replaced easily at any time if you want.