With my build, I'm finding that my feet are up against the bulkhead slightly pointed.

Would it be better to take out the minicell and try to get the footrests to fit, put in additional minicell foam. I'd like to get this to fit me right, but am not completely certain as to the best way to go about it.

Gero-
You should check with the rails and footpegs you have there, but I just checked measurements on a couple of types (SeaLect and Yakima) I have on the shelf here.
The closest distance between the end of the rail and the foot peg surface that the foot touches is about 3.5 inches.

If you put the rail end right against the bulkhead, I'd guess that the footpeg will not be far enough forward to match your leg length.

I like to adjust the footpegs so that my thighs are just lightly touching the undeside of the deck when my feet are in a 'neutral' relaxed position. A bit of foot pressure 'locks' my thighs up against the deck.

Unless you want to move the bulkhead forward, padding it out with foam seems like your easiest bet at this point. If there's room, using a wedge shape on the foam (so the surface is at about 60° to the 'floor' aka cockpit sole aka hull) will provide a more comfortable foot position IMO.

An alternative to foam would be a DIY 'footboard' - something like the 'Flow' commercial ones (without the hinged rudder controls) or a one-piece version of what I made for my Thomasson Panthera.