Little back story I had a artificial disk put in at L5/S1 and arthroscopic hip surgery for FAI.

31yo 6’1” 240lbs is like to get weight down to at least 210.

I’m not able to do the 5x5 routine I get increase in back pain doing the squats and dead lifts even using good form with just the bar.

Up until recently I have been able to ride a bike but a new knee pain has started up and now that’s limited.

I’m not sure what direction to go in to get in better shape to preserve what’s left.

Keep up with the bike. High resistance and low resistance, high speed. That new knee pain is because you are not used to it. Take time to stretch.

Go to your local planet fitness, tons of machines there to do some light lifting for an hour. Then ride your bike home.

Get one of the "Tommy Copper" knee sleeves, has helped me when I go to spin class. (Try to go twice a week.)

As an added note..

Weight loss is all about what you eat. I workout all the time, but if I eat like shit, it's pointless.

What sort of activity are you cleared for by your doctor?

Generally, in normal healthy people, building muscle relieves the workload from the joints and helps minimize pain. Getting to that point can be painful though. If you are cleared for lifting I would research and seek out a good coach that has experience working with injured people. In my case I found an awesome chiropractor that focuses on strengthening the right muscles to prevent future injury/reinjury.

Bike riding isn’t new I have been doing it for over a year,

I’m cleared to do most things can’t run because of the hips or axial loading lifts. I have lost some weight with diet, but getting up and moving causes less pain in the back then if I don’t do anything.

What about swimming? It's about as low impact as you can get.

For losing weight, get your diet in check, you can drop 30 lbs without even getting off the couch if you dial your energy intake in.

To avoid overuse injuries, engage in a variety of activities.  Bike, row, walk, elliptical, XC ski, swim.  Do most at relatively low intensity and, if you can, do some sprint-type work once or twice per week on the bike or row.  If something hurts cut back and substitute a different exercise mode.

Do what lifts you can do without pain a couple of times per week.  Try a yoga class.  As you lose weight and improve flexibility, you may be able to incorporate more activities.

Diet, swim, DDP yoga.

Where exactly is the pain in your knee?  If it's in the front it's because your peddling technique is wrong.  Even though the ball of your foot is on the pedal you need to push with your heel.  It's the same with any leg pressing movement such as leg presses or squats.  Press with your heels not your toes. This takes the stress off your knees and puts it where it should be, on your muscles.

Knee pain is all over hurts when standing or if I pivot while walking to turn or when bending. I can’t recall any event that would of injured it and never had a sudden sharp pain in it. It’s not just activity based it’s all the time.

When using the toe of my right foot to take off my left shoe at the feel the left knee hurts or when using my legs to pull back on the leg extension on the recliner.

On the squat, some people who cannot back squat have no problem front squatting Zerchers.  Belt squats as well.  I wonder how much strengthening the area and increasing flexibility would be in relieving the pain in addition to benefits of weight loss.

I know a lot of people that had knee pain from being weak in the glutei causing Pelvis and Femor alignment issues which adds incredible stress to the knee.  Also general weakness and lack of flexibility incredes stress to the joint.

I tried front squat and It caused the same pain. I do clam shells with bands, lateral leg lifts, glute bridge to help with the hip and glute strength as well as a balance board.

I’m not as consistent as I would like to be do to work.

OP, I have had meniscus clean up in both knees, can't run over 100 yds without pain...start squatting low bar first, focus on learning the technique well.  I can front squat now, but it does hit my knees a lot harder than low bar.  My knees feel better now that I have built my quads and legs up overall, still can't run though.

Swim

Lots of good advice here.

The one piece of equipment that has the single most positive change to my training has been my Rogue Air bike.

With my knee pain, ongoing low back pain and just had my 43rd birthday. it's been a game changer for me. (I also have a Concept2 rower but it did not have the same effect as the bike)

The Rogue Echo AirBike has improved my fitness in multiple ways. It's a full-body workout that taxes both your cardio systems and your muscles. Everyone at my bootcamp that I run have a love\hate relationship with it.

I use it with seniors that I train with as well and they all love the quick and effecient workout it gives.

If you can swing the $700, I would highly recommend it....

https://www.roguefitness.com/rogue-echo-bike

Both of my knees are trashed and my 2 lower discs are smashed too. If I don’t get in the squat rack at least once a week I get to where I start hobbling around like an old man. Neoprene knee sleeves help a lot for me.

That’s where I’m conflicted on it. I don’t have pain while doing the squats. It’s afterwards that it starts leading me to believe I’m not hurting that area, but it’s a decent amount of pain so I am hesitant.

Lose weight now. I would recommend intermittent fasting and watching the types of food.

At the same time, natural anti inflammatory products.

I've got bilateral FAI as well as 10+ years arthritis damage in both hips.  I'd been looking at hip replacement or arthroscopic surgery to correct the FAI.

The pain was so bad while warming up on squats I'd usually rate it at a high 8 on a 1 to 10 scale.

Everyone but my wife said stop squatting.   She convinced me to shell out the dollars for a Starting Strength squat camp.  The SSC coaches there fixed my screwed up form and it made a world of difference.

I can now squat without pain,  the FAI is still there, the arthritis is still there.   What's gone is the hip pain.

I'd hazard a guess that like me, you've got a form issue that's cascading across your body.   Fix the form and see what happens.

Semper Fi

Heavy compound lifts are a young and healthy man's game. Furthermore extended cardio sessions puts extended strain on ligaments/joints. I don't know what kind of time you have on your hands and how far your willing to go. But assuming you've got time and motivation I'd strip it down to a basic bodybuilding routine.

In the mornings go for a 30-45 minute walk at a moderate pace. Or try to cycle, again at a moderate pace nothing intense that would cause pain. In the afternoons/evenings hit the gym. For major muscle groups (Chest, back, legs, delts) do 16-24 working sets per week. For accessory groups (Abs/Bi's/Tri's/Traps/Calves/Forearms) 10-12 working sets per week. Stick to 10-12 rep ranges.  Focus on a full range of motion and getting a good contraction in the target muscle group. You could either do: Chest/tri, back/bi, legs/abs, shoulders/traps. Or something like Chest, Back, Legs, Shoulders, Arms. (Depending if you want to lift 4 or 5 days per week).

Only do exercises that don't cause pain. Focus on proper contraction and over-all volume. Be consistent. Clean up your diet/nutrition and cut processed foods out. Try to time your rest periods and keep them at 30-60 seconds. If you need longer then that you need to lighten the weight your moving. Focus on your breakfast being a higher calorie meal. An hour before you lift get a good meal in with a lighter protein (Chicken, fish, etc.) and a quick digesting carb (White rice for example). After you lift (within the hour) try to eat again. Carbs & protein, perhaps a mirror of your pre-workout meal.

Your at an age where health and how you feel is the priority and then I'd say how you look (Because that can affect how you feel) comes next. Athletic performance, being really strong, etc. are all after all of those. In my 30s now and those are the principles I follow. I do one compound movement for each major body part with a barbell or DB (But still light because its 4 sets of 10 reps). Then everything is either lighter DB's, Cables, or machines at 12 reps. Feel great and in the best shape of my life. No nagging injuries/pains. Which I had when I focused on performance/strength training.

[/edit] If you have pain with squats and compound lifts don't do them. Machines will be fine. You can still progressive over-load over time.