Late Salary Normal? (among other issues)

As the question states, this is the second time out of five paychecks that I'm receiving my salary delayed. My company doesn't seem to want to set up an automatic deposit system, so I have to receive my salary in cash from the assistant manager...but the main manager (who refuses to issue paychecks himself) often schedules her off on pay day and/or the following day. I'm supposed to receive my pay on the 15th, but this month it won't be until the 17th at the earliest. It's not that late, but it's just annoying when it could be an automatic transfer.

I'm having a few other issues with this company as well - a poorly maintained company dorm where my requests for improvements (like windows that don't shut completely and a broken heater) are denied, being told that I don't qualify for any paid leave until Feb 2018 because of a company policy that I think is illegal, being scheduled for 10 hour shifts and only getting paid for 8.83 hours because of an extra included "break" that we often don't get to take, getting my only sick day deducted twice, verbal abuse from my manager, vindictive shift making (like putting in a request and getting the opposite), etc.

I could tolerate each of the problems individually, but adding them together...I'm not really sure how to approach the situation. Does anyone have any advice?

Changing your job seems a good option.

Sounds like a textbook black kigyou. Talking to your Labour Relations Board is probably not a bad idea, and they might help get some of the issues ameliorated. But, ultimately, you're probably going to be wanting to look for other places to work.

Not giving paid leaves for the first six months is legal.
And the "break" thing is also legal. Just take a break following labor law. What you should claim about is not salary, but is not letting take breaks.

My guess is that they want to pay cash because they have two sets of books - showing a higher payout for tax purposes. This itself probably isn`t a big risk for you - except when you eventually do give notice. You might find that the last payment is `light`, or even missing entirely. Just make sure that you do keep your payslips if they are included with the cash, or keep an accurate record on your own.

"being scheduled for 10 hour shifts and only getting paid for 8.83 hours because of an extra included "break"."

if not saying more precisely, it can't be judged.
if you are in assembly-line or something similar, about 1 hr rest at noon, and two short rests in the morning and the afternoon are pretty common. they don't need to pay for the resting periods.

"getting my only sick day deducted twice"
if you mean that they don't pay salary for your sick day because of your absence, it is quite ordinary. being sickness is your fault.

"Not giving paid leaves for the first six months is legal."
I don't think so. according to the law, paid holidays should be given after the first six months. No giving for the whole one year is illegal.

irregular salary payment means a typical bad company, probably they have financial problems.

what working status do you have ?
aren't you 技能実習生 ?

The more important question is: are other coworkers treated the same as you are, or are you being singled out?

If everybody is in the same situation, then the company is mismanaged or worse. Look for another employment while you still have the current one.

If you are being singled out, then they may be trying to tell you something - perhaps they are trying to make you resign voluntarily.