Make photo copies of your old passport including all stamp pages. Once you receive your new passport, go to immigration and have them transfer the stamp. If you've never activated your LTR (entered using that visa) then I'm not sure the visa would be valid against a different passport number. But you could make you case with the IO upon entry...
I found i had to leave the departure date blank otherwise it thought arrival/departure were the same day and that meant you were in transit, not staying in Thailand. Site logic is bad. Couldn't enter the accomadation data until i dropped the departure date. Note, i was trying to do this enroute from USA so guessing the dateline had something to do with it...
Note 2, remember to print and keep the document, you might need it is you apply for an extension of fire s be visa in country...