I'm sorry about your problems and it does sound like you will be paying those jobs out of your own pocket. Keep your receipts, though, as they will be deductible as a business expense on your taxes even though the reports were not accepted and paid/reimbursed. Stuff happens. Your experience is one of the reasons why many MSPs will not assign high reimbursement shops to newbies and I always advise newbies to never do a job with a reimbursement they can't afford to lose.
In the first case you didn't mention if you had contacted or attempted to contact the scheduler. It might or might not have done any good since the visit was complete, but it might keep you from being marked as an "unreliable shopper".
All the mystery shopping companies are in a bind themselves with late reports because they won't get paid if the results aren't sent on to the client quickly. Deadlines loom all up and down the pecking order. I have one editor who generally gets back to me within an hour and a half of when I submit a dinner report. When I don't get finished until 1AM, she still will have an approval or request for more information in my mailbox by 2-2:30AM. Although I could wait until the next day to respond, I usually stay up until I hear from her so she can get to bed too. One of the hotel/resort places I do reports for must have the information to the client 24 hours after I check out. That means I need to find an internet connection to finish the checkout and departure part of the report usually within 4-5 hours and get the entire report uploaded, including massive narrative and photographs. I've just about missed plane connections in airports because the upload is going slowly and I won't be on the ground again until after the deadline. And if I am late, everybody else has to work overtime.
If you scheduled these shops directly with the mystery shopping companies, you may still be okay with other companies. If you scheduled them with a scheduling company, you may be declined for jobs with any of the companies they schedule for. A reputation is hard to build and easy to damage.
Generally for a restaurant shop you will be required to purchase specific types of items. Failure to purchase any of the requirements or tip at least the minimum required amount will invalidate your shop. I rarely accept restaurant shops from Second to None or from Bestmark because a quick trip to the menu on the client website will show you that their reimbursement will cover only half to two thirds of the required purchases (at least in my market). Life is a little short for just a subsidized meal and a long report.
Equipment failure will always be a problem and requires creativity. I have an old printer/scanner I keep around as a backup. I can take photos of receipts with a digital camera that are legible (and CPIs in a bind). I have both a laptop and a desktop and if one is flaky, I can still use the other. Our internet connection is by satellite and goes out when there is heavy cloud cover. I know a half dozen businesses in my area where I can sit in their parking lot and catch enough of an internet signal to do a report. There are also the restaurants, including an all night IHOP that have free internet access for customers, so I have enjoyed coffee and pie until 3AM putting in reports. Then there is FedEx/Kinkos where you can rent time on their computers 24/7 and of course the public libraries if you have needs during their open hours. One in my area has even made their internet access wireless. And when all else fails, I have thrown myself on the mercy of a nearby hotel where they were amused enough by my plight that they didn't make me rent a room to get a passcode for their wireless access.
Schedulers and editors hear excuses all day, every day. Almost every call or email is a request for an exception of some sort. Remember to take a minute from time to time to drop them a short, warm fuzzy note. Keep it short and sweet and completely without demands or requests. It will help make their day.