Is Calorie Intake correct?

From 2011 to 2012 I used this site for 1 year and lost 103 pounds. I was sedentary, so my calories were based on if I hadnt ever gotten out of bed each day. I logged any extra movement, like anytime I washed dishes, or cleaned the house, or cooked a large meal..hell even if i had to stand for a long period of time somewhere. And while Im sure alot of people disagree with that type of logging, it worked for me. I (almost) always ate back all my calories, I never went over, and having it set for a 2lb a week loss, by the end of the year the average weekly weight loss was 1.98lbs, so right on target. I never used a HRM, just whatever MFP said.

2012, and 2013, was a couple of rough years (I moved 5x between the 2 years, relationships ending/starting, loss of job, unemployment, new jobs, new jobs ending, new jobs starting, etc...), and I lost my motivation and ended up regaining 45lbs. Im now back at it now that stress has went down and im stable, but now im working a job in production.

I work 12.25hr shifts (or 10.75hrs after breaks are removed). I am standing the entire time, and walking back and forth for a decent part of shift on most days (somedays can be different, so I didnt want to put it to Active just Lightly Active to make up for those days that arent as physical). The difference between sedentary and lightly active is just 220 calories.

If before when I lost all my weight, I logged say, cleaning, for 1 hour, Id burn 282 calories, Or walking in the grocery store at a 2mph pace for an hour, another 282 calories (564 calories for only 2 hours), and ate back those 564 calories, I still lost my 2lbs... but at work now i could clean for 2 hours, walk for 5 hrs total, and stand the remaining 3.75hrs and im only burning 220 calories? If I set it to sedentary, and entered in those numbers, I could burn up to 3000 calories a day depending on the day. Even if I just stood in place and never did anything else its 1500. No where near 220. (or even if I moved it to Active--its only an 390 calorie difference to sedentary. How is this anywhere near accurate for anyone, even if they had normal length shifts?

I eat alot (almost all clean eating), dont think I could eat that amount if I wanted, but it makes me worry if Im eating enough. At the end of the week my body aches and hurts, its hard for me to find motivation to do much else. I have to drink coffee to go to the gym on my days off (before when I lost my weight, I never once drank coffee or did any energy boosting supplements or anything. I try to have extra protein now (never counted protein before), because its suppose to help your muscles, but the lowest protein ive had all week was 85g, and usually between 110 to 155g (MFP suggests 61...85 on days i work out). I know part of that has to do with working such long shifts Im short changed on sleep alot due to my 2hr drive time, but even when I catch up on sleep on a weekend, I still have to force myself to do things. I never had energy or motivation problems before; and before I wasnt clean eating (clean eating gives you extra energy in itself--again im not fully clean eating but in a week i might just have a couple/few things not clean but pretty close to clean). I still go to gym every day off, but then it just pushes my body into being extra sore for work, and by the time I have my next day off Im dead; and the cycle continues week after week. Could this issue be calories? Its also very warm at work and im constantly sweating-even on days i dont feel sweaty ill get home and my clothes are drenched, so I think I burn more calories from that too? I drink 14-20 cups of water a day.

Any help or suggestions would be great; I just want to be healthy and want to make sure im providing my body what it needs, without using a HRM (I cant afford one/low income).