How do I get a permit in the Sierra Nevada now?

First step - always consult the jurisdiction into which you are venturing. The wilderness permit, if one is needed, will always be issued by the forest/park in which the trailhead you start from is located, with a few exceptions.

Inyo National Forest (Ansel Adams and John Muir Wilderness, some Golden Trout trailheads, Hoover Wilderness, including Mt Whitney):

Sequoia National Forest (Golden Trout Wilderness, Jennie Lakes Wilderness, Monarch Wilderness):

Neither Monarch nor Jennie requires permits but you will want to review regulations. If heading into Kings Canyon or Sequoia NP from Jennie you WILL need a permit from SEKI via their reservation process. Golden Trout requires a free non quota permit available remotely.

Sierra NF has a mail-in procedure for reservations. Walk ins are taken by phone the day before your start date and left in the night box. If you do not mail the application at least three weeks in advance you will need to wait til the day before and call for a walk in.

In national parks your wilderness permit is your fire permit. In national forests, obtain a California fire permit.

Even if there is a fire ban you need the California permit to use your stove. Always check current conditions and regulations - seasonal fire bans that prohibit all open flame including stoves, cigarettes and anything that sparks do happen in some areas. There are permanent elevation bans on campfires that differ from one jurisdiction to the other.

Fishing permits for California are from DFG: wildlife.ca.gov/

All visitors from out of state are required to have a permit to fish and review regulations, which vary widely from one watershed to the next. SEKI has different rules than Yosemite. Some waterways are Wild and Scenic and are catch and release for native fish.