As far as thailand is concerned, a 4 day overstay is no big concern. There will be a stamp in your passport that may cause an issue for other countries, but not for thailand. Fine will be 4 x days at 500thb so 2000thb. As far as your passport is concerned, you need to take that up with your government, maybe a stiffly worded e-mail may do the trick.
Judging by this report, I think we're about to see what he's been up to for the past two years. He was behind an anti corruption drive that made him quite unpopular amongst Immigration officers. He was making some headway when he was removed from his position.
you can get a 60 day tv extendable for 30 days giving a total of 90 days. Employment is prohibited on this visa. As an aside, the documents shouldn't take more than a few hours to put together. I would challenge your employer about this.
It would be far easier for both you and your company to obtain the 90 day non B visa outside Thailand, then applying for the one year extension based on employment. Even with a WP, you can not work if you enter on a tourist visa until the non B has been granted.