Sorry for the delay in answering.
1. Depending on where you are, and how hot the roof gets, the standard space of the L-foot plus the width of the rail is generally enough air space between the roof and the panels. If you are in extreme heat, additional standoffs or a longer L-foot may be helpful to increase air flow and keep the panels cooler. For metal roofs, I like the EcoFasten L-foot with the EPDM bushing to help seal the hole. They are available in 3" or 6" lengths, for a higher mount,
https://www.altestore.com/store/Solar-Panel-Mounts-Trackers/Roof-Mounts-for-Solar-Panels/Flashing-for-Roof-Mounts/EcoFasten-Solar-SIM-L-102-6-Tall-L-Foot-with-Simple-Seal-Bushing/p11108/ .
2. It depends. There are calculations to determine the length of the lag bolt needed that include wind loading for your area and type of wood for the rafters. Let's assume 10.6 sqft per panel and 4' spacing between L-feet (3 rows of 11), that would require 60 roof connections. Assuming the array needs to withstand 50psf wind uplift force the equation is 50 psi x 10.6 sqft = 530 lbs per panel x 33 panels = 17,490 lbs for the array / 60 L-feet = 291.5 lbs per L-foot. There is a chart in the Wood Engineering and Construction Handbook for what length Lag bolt is needed based on if the rafters are Southern Yellow Pine, White Spruce, or Douglas Fir. For example, a 5/16" bolt in White Spruce can handle 227 lbs per inch. 291.5 lbs / 227 lbs = 1.3" of the lag bolt must be in the rafter. Add an inch for going through the L-foot, roof, underlayment, etc, and you need at least a 2.5" stainless steel lag bolt. I'd use 3" for good luck ; )
3. Yes, use stainless steel lag bolts.
Amy Beaudet
Solar Queen
altE Store