We've all got our crosses to bear.
Generally speaking, without proper extension range at the big toe, the following ramifications (or a variation there of) can take place:
compromised hip extension
over activity of hip flexors
possible trigger points along the iliopsoas (this could be the cause of your hip flexor woes)
possible lateral flexion which can lead to leg length discrepancy
over activity of contralateral quadratus lumborum, internal/external obliques, ipsilateral tensor fascia lata and IT band
potential issues with contralateral sacro iliac joint
potential issues with contralateral piriformis
If you're not dizzy after reading all that, the take home is you've got some work to do - rehab and prehab work that is.
Generally speaking, unilateral movements place a significant recruitment on the adductors and glute medius of the squatting leg and contralateral quadratus lumborum. It's also a nice way to deload the spine.
I do NOT recommend the pistols in which you basically sit on the calves. It's much too easy to relax the muscles and place all the load on the connective tissue.
A better option - one that I coach for those who have no contraindications - is band-assisted single leg squats off a box. The box will allow the non working leg to relax a bit more as it does not have to clear the ground. After all, it sounds like your hip flexors are over active.
Also, using the band (hung off pull up bar or similar) allows you to sit back and finish with a vertical tibia when in the hole. This vertical tibia, as I stated in another thread, makes the movement more glute dominant. This will help you more efficient neurally with the glutes.
As your strength improves, progress onto a lighter band until you can do the movement with body weight - at which point it will be near impossible to keep the vertical tibia in the hole. When this happens, you have the option to use this as a post exhaust with bands (again, this can now be safely turned into a glute dominant move). Even when you are strong enough to do this at bw or higher, you can incorporate the band on your repetition/volume days using methods such as 1 or 2 reps half way up and 1 full rep. I've done sets in which I do 10 "pulses" in the mid range followed by a full rep. Because I don't have a loaded bar to deal with, I can relax the diaphragm and breath during the 10 "pulses" - performed with a slow eccentric, this type of training can be valuable.
Also, you can do step ups with a controlled eccentric. The nature of the movement will allow you to choose the tibia angle and make it more or less glute dominant.
Unilateral RDLs can be another viable option.
Not only do you need to address the plantar fascia, you need to address the soleus and gastrocs as well. Given your situation, there could still be some room for improvement in terms of greater range there.
How do you perform the hip flexor stretch. A small adjustment such as NOT extending at the lumbar spine can help because the lack of extension increases the distance from the origin (T-12 to L5) to the insertion at the femur. Greater distance between two points - without causing injury - equals a more effective stretch.
As for releasing the trigger points at the iliopsoas complex, that's where a skilled therapist can be valuable.