You just resumed riding. It'll take awhile to get back into shape.
Meanwhile, do some range of motion exercises to strengthen the arms and torso. If you don't already do full floor pushups, etc., start out easy with wall push-offs. Then countertop push-ups. Take a couple of weeks or more before trying full floor pushups.
I have chronic pain from various injuries, including a busted up neck and shoulder. Periodically I'll get lazy and skip my usual full body home physical therapy exercises. Recently my shoulders, neck, lower back, wrists, elbows, etc., have been a bit achy. But I haven't done any arm or core exercises in two or three weeks. Usually I'll do those exercises midway through my usual 5-7 mile jogging route, stopping at the top of a climb to do some exercises on grass under a shady tree, but it's been so hot and humid I've skipped those mid-jog exercises. So I'll start back easy, with countertop pushups, etc. Then resume floor pushups after a week or so.
When I'm jogging I always carry water in summer. Usually a hydration backpack but occasionally a water bottle. If I carry a bottle I'll use the weight of the bottle to work both arms, shoulders and elbows for warmups during the first mile. It's only about a pound of weight but enough to help loosen up the arms and shoulders.
In cycling we never approach the effort needed for floor pushups, so it really isn't necessary to do more than angled pushups off a countertop, or wall push-offs if we're really out of shape.
There's planking too, which I find incredibly boring, and it tends to duplicate the position we're already in on the bike. Even if I plank for a minute I don't try to stay rigidly still. I'll vary between elbow/forearm supported planks, hand supported planks, and flex the hips, along with easy range of motion exercises for the legs.
My physical therapist feels the same way about planking. He thinks long planks are pointless for cyclists because we're already doing similar exercises merely by riding a bike. When he had me doing neck exercises, he suggested avoiding the types of exercises that duplicate working the muscles already being worked by cycling. So we focused on working the muscles that are usually neglected in cycling. It helped.
Ditto, those workout rubber bands. I have several but seldom use them. They do help if I remember to use 'em.