Phuket immigration also keep the passport for one night for retirement extension, but at least you have the receipt. So you can show the police where your passport is.
Um... with 90 days you mean the 90 days report? Yes... that starts everytime new when you enter the country. For the visa it's what John said already... expired is expired and "re-entry" is different to "multiple entry".
You can't renew your visa, you can apply for a one year extension. This you can do when you have 30 days left on your last entry stamp, some immigration offices allow 45 days.
A multiple entry tourist visa could be an option. It's valid for 6 month, gives you 60 days each entry and you can get one 30 day extension. After that you have to do a border bounce and you will get another 60 days (+30) and so on. If your timing is good you can stay almost 9 month with that.