Im making a removable set of lights for my flat bottom. I want to put a 3 inch wide by 26 inch long piece of 3 inch flat stock to mount a lightbar across 2 of those big suction cupped handles for moving panes of glass that i can suction down to the front deck when in use and remove when fishing during day time. The handles are painted aluminum and the steel is unpainted.
I dont think i want to try to bolt these together as i would want to use stainless bolts and ive heard when mild steel is attached to aluminum, the aluminum can become corroded? Would JB weld be a good option? Some other adhesive? Also wondering if i would need to remove the aluminum’s paint.

I would remove any paint from surfaces to be bonded.
3M VHB tape would probably be a good solution here.

Get a sacrificial zinc anode. Might help.

First, I'd use aluminum for the bar and assemble with SS bolts (tapped) or nuts.
If using the steel, I'd still use bolts leaving the paint as a barrier and maybe add a mylar, or other plastic shim as an additional barrier.
The steel will rust quickly, and is heavy. I'd worry more about that than the cup handles.

What Crowfoot said. Any strickly bonding agent could never be absolutly trusted, and your lights may suddenly pop off and go in the drink, with their own anchor! Use a heavier piece of aluminum and bolt like Crowfoot said. If what you are attatching to is real thin, find some nutserts to install, or if you can get to the back side, back it with a heavier piece and use stainless locknuts.

A piece of butyl widow flashing tape between the two surfaces would prevent any corrosion, just apply to the bottom of the bar and go from there.

I'd shy away from just JB weld
Take the advice given ^^^

The process is electrolisis, and will eat up the material fairly quickly. Why do you want to use steel instead of aluminum? A piece that size will be very heavy. Might consider a piece of PT 2x4 instead.

I know aluminum would be better. Had just plan ed on painting the steel. Reason i was thinking steel is i have absomutely no way to cut down a sheet of aluminum and i can readily find 3 inch wide steel. Anyone know an online source for 4 inch or narrower aluminum?

Online Metals .Com or Metal Supermarket.

This^^^^^^^

I'm not sure what you have in mind but you can cut a sheet of aluminum with a circular saw.
just

Most any industrial supply house can sell you what you want, in about any size, and cut to length.

You can buy short pieces of aluminum flat bar at TSC.