I'm assuming the 'small tablet' you refer to is a medication called omeoprazole? I was first prescribed this over 20 years ago for a doudenal ulcer and gastric reflux. After several years I was given a lower 'maintenance dose' but the reflux problem returned. Since then I've been on 20 mg of this for several years without any problems running or not. So, indeed it may be that you do need a higher dose. For me I just considered it better to be able to carry on running than worry about having to take more medication. Speak to your doc about this, but its up to you how you want to find the happy balance between keeping healthy with running and 'having to take pills'
Pain on the inside of the knee is a common symptom of patella femoral syndrome, or as they called it in my day 'chondromalacia patella.' I suffered from this way back in '84 and the treatment was to strengthen the vastus medialis muscle (inner thigh) in isolation with short range leg extensions using a loose weight strapped to the ankle. This worked very well for me and I still do them to this day. The idea is that you put a weight in each of a pair of socks,(eg: tin of beans) tie them together and hang them over your ankle. Sit on the edge of a bed or settee and straighten your leg out to full extension whilst pointing your toes up hard towards your face. It's just the last few degrees of angle that isolate the vastus medialis, hence the socks so you're not taking up the load too early. Also, ice after running and I used ibuprofen gel in the early days until it all cleared up.
However, I would run this message past your physio first before trying as treatments and ideas change over the years. All I know is that I'm still here, still running after all these years with no knee pain.
If you have custom made orthotics these must be put in a neutral shoe or as you say you are altering the motion control that they were designed for. Surely your podiatrist that prescribed them told you this? The shoe insole must be removable also, some running shoes have fixed insoles, you must be able to replace the one that came with the shoe when you bought it. Other than this what worked for me was regular ice application (rolling a cold coke tin under the arch) and calf flexibility. The stair stretch was prescribed and worked particularly well for me, This is where you stand on a stair with your feet shoulder width apart and heels overhanging and slowly lower until you feel a gentle stretch in the calves and under the arch. Don't bounce, just lower slowly. Good arch support is important and I trust your physio/podiatrist customised your orthotics with this in mind. PF imflammation takes time to settle down so don't rush things. Personally, I don't think lashing out on overly-expensive trainers is the answer, more to so with overtraining (too much too soon) Get professional secondary advice before trying any stretches/exercise. I only know what worked for me. Good luck.
I had very similar symptons to this some months back. I saw a pro-rugby physio who never gave the problem a name but diagnosed weak glutes and over tight quads putting tension on the hip. You can test the quad theory by trying to roll the outer quad on top of a foam roller. If this is very painful (as mine was) then your quads need loosening up. Daily foam rolling, active isolated stretching and single leg bridges (for the glutes) did the trick for me. Be sure to ask your physio first before trying any of these as your problem may be of a different origin than mine. Good luck.
Unfortunately GP's are not all sports oriented, I was once told to stop running...30 years ago! I sympathise with your plantar fasciitis problem, it can be a real b*****d to get rid of. Five months is not uncommon, mine took longer than this as I didn't get the right advice to start. Anyway, this is what worked for me: daily ice, using a pop can rolling and massaging the fascia. Calf flexibility is the key to this one. A physio got me doing the stair stretch but gently to start. This is the one where you stand on the edge of a step with your heels overhanging, slowly lowering you heels and holding for anything up to a minute. Go steady and don't just suddenly drop your heels. Keep your legs straight and don't bend at the knee, I was told this puts too much stress on the fascia. Ask a physio or your podiatrist about this, I can only say what worked for me. As for orthotics I wear Scholls orthoheels in both my running shoes and workboots as I tend to have flat feet also from standing all day. These are available at Boots and other chemists and in my opinion are as good as any custom orthotic for a lot less money. I haven't had plantar fasciitis for the past six years. Good luck.