I got the inspection plate off, video coming, looks pretty good, but I would like to freshen up the seam sealer around the base. I have some butyl seam sealer that would work great where I can get to it but the back and the side towards the middle of the car have very limited access. I am thinking plumber putty, make up a rope of it and snake it back then work it in.

 

I wouldn't use plumbers putty! I would use a sealant of some kind. If it's in a caulk tube you can put a short piece of fuel line on the end of the caulk tube so you can get the material in place.

Use Duct Seal. Best stuff ever. All electricians, plumbers and HVAC use it to seal penetrations.

Never hardens. A 1 pound block will last forever. You will use it around the house too.

Example here. 

https://www.amazon.com/Gardner-Bender-DS-110N-1-Pound-Compound/dp/B000BO8XD6/ref=sr_1_2?ie=UTF8&qid=1472663530&sr=8-2&keywords=duct+seal

too late plumber putty was done right after I posted.  the cover is removable so will check on periodically and report back. Patcon the prob with any kind of sealant that is even remotely sticky to hands is the problem of getting it in place in the back of the chimney. I had to work it with my hands/tools/anything I could lay my hands on to try and form it. I ended up using a plastic dowel to reach the last bit that I could not squeeze my hands into. I don't think I could have enough control with a delivery system that used a tube. I know plumbers putty never hardens, I painted over it anyway. The Lumens stuff looks like a good way to go. I was planning on using my butyl caulk but after using it on the windshield there was no way I wanted to mess with it with limited access. It hugely messy and gets everywhere.

I learned a trick from a commercial glass installer on poly butyl.  They used Dollar Store Palmolive dishwashing detergent on their fingers and putty knives to smooth it out.  It won't stick and pull when using that.  I use it on my fingers smoothing silicone caulk.  Works great.

I know there is very limited space there. I dealt with that area a couple of years ago...

Site,

I use denatured alcohol on my fingers when working with silicone. It works great too...

I need really much smaller hands or longer fingers

anyway its all buttoned up now, used some SS screws like one the sill plates. I will check on it if I see any signs of failure, at least it should be easy to scrape off.

if you have a water leak (you didnt really say) that plumbers putty isnt going to last long at all. its simply not made for that.

no water leak, no rust, just some cracks starting in the orig sealer, a few small chunks missing.

No leaks? Looking at the route of the storm, you might find out for sure tonight if you go on your regular neighborhood tour!! Just like when we tested your windshield. 

Stay safe!!