Apart from the quarterback controversy, the main questions surrounding the San Francisco 49ers have been in regards to the inactive list. Namely, what is the purpose of carrying Brandon Jacobs and when will A.J. Jenkins and/or LaMichael James get to wear pads for the first time in an NFL game?

Goodbye superfluous depth, hello new contributors.

Now that we know the extent of the tears suffered by Kyle Williams (ACL) and Kendall Hunter (achilles) on the same play, the question becomes this:

How will the 49ers replace two key role players who are now on IR?

Hunter may have benefitted from one of the best (The best?) offensive lines in football, but 5.2 yards per carry is 5.2 yards per carry. How good has Williams been? People were clamoring for him to start returning kicks and punts on Sunday, just three months after I wrote a post urging Candlestick Park patrons to stop booing Williams. He’s also the team’s No. 5 receiver in terms of yardage and has caught the longest pass of the year (that 57-yard bomb from Colin Kaepernick against the Bears).

Replacing KH

Jacobs got his first two carries of the season in New Orleans — the first was negated by a penalty — and stands to receive several more. After looking dynamic during the early stages of the preseason, Jacobs should now be highly motivated to prove that the 49ers made a mistake in not utilizing him sooner and that his career should not be over at the conclusion of this season. Anthony Dixon will also see more action on offense, as the 49ers don’t want to overextend Frank Gore before the playoffs.

However, neither Jacobs nor Dixon closely approximate what Hunter brought to the offense, and Jewel Hampton (activated from the non-football injury list today) probably won’t play unless another running back gets injured.

What about James?

It’s an interesting question, especially with Kaepernick *probably* taking over as the 49ers’ starting quarterback. As Joey “Bay Area Duck Guy” McMurry pointed out in today’s BASGcast, Hunter was an integral part of those read option plays the 49ers love to run with Kaepernick, and James could be used in that role.

In fact, James was on the field alongside Kaepernick in the first preseason game when the 49ers’ quarterback kept it and ran for a 78-yard touchdown. I talked to James after that game about his buddy’s long touchdown scamper, and here is what he said:

Replacing KW

I was extremely impressed by Jenkins during the preseason, and he’ll get some opportunities to show what he can do as a slot receiver. However, I agree with Tre Faaborg of NinersNation that Randy Moss is the one who’ll see the biggest increase in activity in Williams’ absence. The 49ers have been cautious not to overuse Moss at this stage of his career for good reason — the 49ers’ plan is to play 19 games, and they still have eight to go. But he has proven himself as a blocker on numerous occasions and during the Monday night game in Arizona we saw what he can do as a playmaker.

With Delanie Walker looking revived in New Orleans and Vernon Davis, Michael Crabtree and Mario Manningham showing flashes of brilliance throughout the season, the receiving part of Williams’ game won’t be missed all that much. It’s Williams’ ability as a returner (he led the team in both punt and kick return average) that the 49ers will scramble to figure out, especially with Ted Ginn injuring his hand or wrist in New Orleans and muffing a punt.

Hunter was also used as a kickoff returner, so this is a major concern. While James may be useful as a read option back, he wasn’t particularly impressive during the preseason as a punt returner (5.3 yard avg over six returns) but handled himself fine on kickoffs (26.1 yards per return on seven chances).

During training camp, no one muffed more punts shot from the JUGS machine than Jenkins. Unless he’s made major improvements in that area, we’re at least a year away from seeing him back there.

One player who may receive consideration in the return game — and this is just based on watching several training camp practices — is Perrish Cox, who had a little experience returning punts and kicks in 2010 for the Broncos and returned four kickoffs for touchdowns at Oklahoma State.