KL is known to ask for these extra documents. That is why many suggest not to apply there. For health, you will need to show your future plan. Usually medical treatment, doctor/hospital and dates of future treatments
My understanding is you are able to submit online, but you will receive an email in a few days (maybe longer because of holiday), that it is actually rejected. What I believe you received is acceptance that they received your submission, not that that it was ultimately accepted. I could be wrong, so others should
You can not apply until after you arrived in country, as you will need to upload your Vietnam entry stamp. Furthermore, next week is the Thai New Year. Embassies will closed and when open, have skeleton crew. You might end up having to wait longer because of that.
Typically it is best to have the letter state you have permission to work remotely from Thailand, but you can try with something generic. I am sure it has worked for some and maybe not for others. All depends on the reviewer
how did you upload all that? Did you create one PDF or multiple files? You can only upload one document per section. If you were uploading multiple documents back to back every new document uploaded would erase/overwrite any document you uploaded before it.