Ok. Let's start over. There's a reason ICON is $225 and Nick is $125, a part of that is the differential in labor costs and ICON gave you that number because they don't want your business. They're not in the business of fixing up someone's bronco, they buy cheaper broncos so they're not spending money on everything they're going to replace, then they build a new car out of it and sell it. Nick is most likely more on labor, but you get someone who does this for a living. He charges more on labor but will probably have LESS labor to do the work, correctly, than someone who doesn't do this for a living. I would guess that his estimate is fairly close to what this would really take. I think your reputable company THINKS they can do this for $50K, but I would bet they REALLY don't understand what it's going to take to do this unless they've done MANY before. So I'm going to try and itemize your list for you to help you prioritize, and add in best guess on what you're missing, and offer up alternative options for you. This will be based on my build and my studying of many other builds here.
1. More leg room, seats need to be electric, with heated seats. - Min $1000 for used seats with these options from a wrecking yard they don't need to be reupholstered. Custom seat track MAYBE $200
2. Seat belts for the rear bench. - non retractable new - $60. Wrecking yard, $10
3. Navigation and a GPS system. - All over the place. Some people use tablets they mount, some use radio/GPS systems from pioneer, some use full screen Loran systems. Say $500 min.
4. Led lights. To include light bar on roof. - you can get cheap Chinese headlights for maybe $300 (with the kit to wire it up). Real quality LED headlights start at $600 and go up. Tail lights, side lights another $200. Your roof bars are the same deal, Chinese for maybe $200, quality ones are $400
5. Electric windows. - $650
6. Electric power locks and a remote start, plus a really good alarm. See if I can get lo-jack. - again, all over the place. seen them on ebay for $200, quality sets are $400-500.
7. Led light system plus extra kc lights. Maybe even spot lights. Fog lights. - $100's each.
8. Rear gate to hold gas can, full size tire, and extra big jack. Or jack and shovel on roof?? With 37's you need a bumper mount spare tire carrier. The body won't hold the weight. $500 min. Tall jack $79.
9. Tow package to tow my boat and trailer - what's a tow package? Your rear bumper will have a hitch when you replace it. Are you talking additional braking?
10. Possibly stretch body to make it longer but not a 4 door (to expensive) - forget it. Can't do it on the frame.
11. Anti lock brakes. - guessing $1000. You'll have to have your calipers machined to take the senors too - $250.
12. Check to make sure I have posey traction. - whatever you have doesn't matter. It has to be replaces to take your new motor. Min 31-35 spline axles and differentials. You can go Detroit Tru trac, $400 each X2. ARB is $1000 each plus pump - $160. New axles at maybe $175 each X 4
13. 4.5 inch lift with 35s or 37 with 5.5 inch lift. Big difference so we'll go with the more expensive one for reference - Wild horses kit with Bilstein single shocks is $1200. BUT you'll most likely need longer radius arms - $800. Then you'll need to extend the brake lines - $50, new drive shafts - $600, Pitman arm $70, and do some work on your steering mounts - $100, plus new track bar - $200. Tires - $2000 with spare
14. Powder coat frame - $750 for the bare frame
15. Largest gas tank possible with a durable skid plate. - Sherman - $630 with skid plate
16. Truck vault box for the rear. - $200
17. Black LineX for body - $400
18. Tags with Bronco and Ranger on the vehicle. - $100
19. Air conditioning for front and rear. No rear kit available. Vintage air - $1300 Plus controls - $200
20. Icon bumpers so I have storage. - ???? Same as spare tire holder for back, another $400+ for front.
21. New leather seat maybe captain chairs? See #1
22. Power inverter with a spare battery to run normal plugs. $150
23. Navigation and radio with xm serious See #3
24. Heavy duty rubber floor for easy wash out - $200
25. Soft top for when I remove hard top - $600 and you need something to store your hard top.
26. Sound dampening insulation on floor - $200
27. New window seals - $200
28. Adjustable steering column - $500 with the new shaft for the PS
29. Coyote engine with fuel injection or possibility of V6 echo boost - $15,000 plus exhaust system - $500
30. Roof rack with highest weight to include off-road. Reinforce top. - $200-900
31. wipers going from bottom of window instead of top? new SS window frame and hinges - $400. New wiper kit - $200.
32. Full roll cage attached to frame so it is sturdy. Plus padding and grab handles. 6 point or 8 point - $600-1200
33. Winch with rope 12k Harbor Freight on sale $299. Warn - $800
34. air shocks and putting an air compressor or air brakes ??? unrealistic
35. Run flats maybe?? unrealistic with your tire sizes.
36. Snorkel kit for engine. - $300-700 plus modification to fit Bronco.
So you're at $36,850 for parts. Roughly. I would do a conservative estimate of at least 750 hours of work. @ $50/hr that's $37,500 in labor. That's taking all your stuff off, rebuilding your axles to put the new equipment in, reinstalling everything, tuning, testing, out the door. Does not include the paint needed when you do the windshield. Then there's hundreds, if not thousands in additional costs - taxes, shipping of parts, oil/antifreeze, gear oil, nuts, bolts, fuel lines, filters, fuel pumps, upgrading the brake system to handle the 37's, all the little problems that come up. Tack on another $3000 in taxes for the parts and $1500 for the supplies, and $1500 for shipping costs and you're at $80,000. So let's double the labor to Nick's work - $100/hr. add in another $37,500 and you're at $117,850. Not too far off from his $125,000.
Hope this helps you prioritize.