How to fix motorcycle front brakes?

I have a 2001 Honda Shadow Ace (VT750CD). My brakes work but need new pads. The front wheel is already off from something else I was doing. The problem is that the caliper pistons are sticking out a little bit, maybe 1/4 inch. With the new pads installed, there isn't enough room for the rotor to go inbetween so I need to push the pistons in some but I can't just push them in. Is there a problem with the pistons? While I have everything removed, I might as well clean the caliper. Can someone please explain the steps?

Should I:
Unbolt caliper
Pump brake until pistons begin to come out more
Grip and remove pistons
Clean the bore and sand pistons
Put waterproof brake grease on pistons before installing again
Push them all the way in flush before installing new brake pads
?

Should I remove the dust seals/o-rings before cleaning the bore? Any help is very much appreciated.

Why risk your life on a bodged repair?
Take it to a motorcycle specialist and get them to fix it!

Use a C-Clamp to force the pistons back in.

Brake pistons are naturally difficult to retract, that's in the nature of the beast. There are retractors made for the job, which force them back into the cylinder, or sometimes you can achieve it with some other form of clamp. If you're not sure get someone who has the tool and knowledge to do it rather than risk causing damage yourself. You can't afford to mess around with brakes.

The pistons should retract with pressure from a flat tool such as a piece of wood. It is unnecessary, and unwise to remove them. They will retract right back into the bore and allow the pads to fit easily.

Use a C-clamp to get the pistons back in the caliper. If you start messing with the brake lever you're going to blow the pistons out of the caliper and end up with a mess. Then you'll be asking how to bleed brakes next. You should watch a youtube informational video showing you how to do replace brake pads on a motorcycle.

NO… NO… NO… Leave it alone,… Get someone that Knows " what's going on "

Use a c clamp to force pistons back All the way back. Or remount calipers and use a piece of fir or big, flat bar or screwdriver to push them back against the disk.
Did you expect to get new, thicker pads in a hole that thinner, worn pads were in?
Can't get 10 pounds of poop into a 5 pound bag!

Don't Touch lever! Don't grease Anything! , you can get it on disks/pads. Don't remove pistons or sand Anything!
You brakes are your life line, Especially Front.

Just like on a car, you will need to remove the master cylinder cover, and if you can't push the piston back in by hand, then use a c-clamp to carefully move it back in. Try to center it as much as possible on the piston (use a flat bar or something if necessary).

First, you should be consulting a manual.
Second, you should use the old pad with that clamp to make sure the piston has no chance of cocking in the bore.