The front windshield and rear window of my 1971 250 both have such old seals that when it rains it literally soaks the interior. My question: Is it best to use a professional or do it yourself? Remove seal or use a caulking type seal to fill gaps between glass and the old seal? Any advice from the experienced?

My advice would be to use a professional (glass repair shop). If the glass is not properly sealed then it will trap moisture and eventually rust the metal around the window and create more leaks.

i second that advice. and there is also a warranty with the major glass companies.

This really is not a DIY job, unless you *and* a capable friend have experience with these cars. Typically, the work performed by glass shops is only warranted if you are buying new glass. There is always the possibility of the old glass breaking, but get some referrals about who does quality work in your area and you'll probably be fine. The most important thing is to use MB seals. You do not have to buy them at the dealer, there are other sources, but the aftermarket seals *will* leak. Have a pro do the work.

some have had some luck with this
 

Another option is to use a liquid sealant called Crack Cure on the existing seals. See if this link works http://www.improvementscatalog.com/parent.asp?pf%5Fid=140830x&dept%5Fid=240&strFindSpec=&Solutions=&code=

I've never tried it, but it seems a lot easier and cheaper than pulling both windows and replacing the seals.