Been out cruising with my T. Seems to be running pretty good on battery, still backfires on magneto. My question is, when slowing down to stop, should I pull the brake handle back to neutral every time or depress the pedal to neutral position and apply the brakes.
IMO, it depends on how long you plan to remain stopped. If I’m just stopping for a short time at a sign or a light, I just depress the low pedal and hold it in neutral. If I plan to let the car sit for an extended period, I still press and hold the low pedal, stop the car, then pull the brake handle back to engage the parking brake. I’m then able to remove my foot pressure from the low pedal and the car will remain stopped. 
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The reason I asked this question is that I’ve heard a clunking sound when stopping. Took it for a ride today and it started clunking all the time, sounds like gears grinding too ,stopped moving altogether. Makes a clunking sound when just rolling it into the garage, HELP!!!
Not good, try jacking up the rear wheels and pull in and out on each rear wheel to see how much play is there. If it is 1/8 inch or more, you may have an old babbit thrust washer inside the rear axle housing going out, which would point towards the need for a rebuild with bronze washers available from the Model T vendors.
Thanks for Mark, I was thinking transmission, but it makes sense that it’s the rear end. I have a spare rear end that came with the car. I’ve taken it apart already just to see if it was usable. The babbit thrust washer in it was in a million pieces and had chewed up the ring and pinion a little. Probably why it wasn’t being used. I watched a video on YouTube by One who collects about rear end rebuilding and apparently the spare one I have is from a 1915. It’s one with the newer style gear housing and older style brake plates, no reinforcement gussets. He said they only made that rear end style for about 6 months. I don’t want to use it in my 1920 car, so I’ll rebuild the original. Going to look in the transmission first, just to make sure, but after you said that, makes sense it’s the rear end.