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Maybe someone else will chime in as to changing some of those LED's back to incandescent. I have not done it yet, but I will as I prefer the lighting a bit less intrusive.
In my recent Spider-man I pulled out all the LEDs. I did not like the overglow on inserts. I had no issue with the result. I don't mind the warm white (others hate it and like the stark (cool) white. However, on SM some of the white inserts are lit at partial power to indicate a 2X or 3X muiltplier. LEDs don't handle that very well and so bulbs are preferred at least for the white inserts.
If you want brighter neat lighting try adding some LED lighting strip under the apron in behind your flippers above the outhole opening (or across the backboard at the very top, underside lip). They don't flicker as they are on steady power and are not seen directly from the player's position.
Also, coloured incandescent light bulbs can add a lot of pop. Add them to your GI lighting without inducing the flicker/shimmering that LEDs can bring. Using red, green, or amber ones in inserts works well. Those plus, yellow and blue work nicely in GI.
POTC below - no LEDs. Incandescent bulbs throughout (except for the factory (way back then!) blue leds at the very top right KEY lanes). Red, blue, yellow, green bulbs were used in GI. From the bottom right there's blue, green, yellow then red(purple?) under the chest and red under the Tortuga ramp. Red at the top backboard for Tortuga progress, Green for KEY (both factory too I think), then yellow and green down the left above the left outlane. I actually ran out of coloured bulbs at the time and wanted to use mostly blue (for 'water') around the playfield perimeter but only had yellows and reds/purples in hand. In the end I just left it as is.
A nice benefit is that incandescent lighting always photographs nicely and never blows out your photo.
LEDs have come a long way. There are some expensive ones that incorporate a capacitor and resistor to simulate a bulb's warming up and cooling down effect, but they still have issues.