LT, both Guard spots, QB, RB, WR (Hill should be a 3 or 4 until he shows some consistency catch the ball), TE (Keller isn't worth what he's going to ask for) on offense need looked at and upgraded if possible. Kerley's a #3, not a #2.
Unfortunately, Sanchez and Holmes are glued here for at least next season. You get to a point that it may be worth just having your cap reduced and dump both or just Holmes and eating the cap punishment.
It is vital to generate some good vibes with the fans and retaining either would not do that.
D-line is OK, would be better with a true pass rusher. The idea of going to a 4-3 plays well with this personnel. Provided they can get a pass rusher.
Wilkerson, Ellis, and Coples provide hybrid DT/DE type players. There's no "elite" pass rusher amongst them though. I'd prefer to get a 320+ LB. DT to play nose then have Ellis play DT. Or keep DeVito. Pouha's probably done at this point.
All LB positions need revamped. Harris is, like Sanchez, probably stuck here, but he's not anywhere near the level of what he's paid.
CB: I like Trufant. He's a good Nickle guy. Lankster isn't bad. Wilson has to go, he's not worth the roster slot. Revis and Cro should end their careers here. I appreciate what you are trying to suggest in that trade scenario, but I don't think it's feasible to move Revis when his value is so low coming off an ACL at a speed position and get a legit equal return.
Lankster isn't a bad dime guy.
S: Both are very good, imo. Landry's a Pro-Bowler, but odds are he gets a contract and then says his Achilles' has flared up and gives you 6-8 games for the next 3-4 years. His pay will be extremely high and this team can't invest any more massive contracts into the secondary.
Keep Bell, offer a 1-2 year deal to Landry, but you can't blow the bank on him, despite him largely being the best player on the team this year next to Wilkerson.
A bad GM will throw him what he's asking and set back the Safety position for years as his Achilles' is not 100% healthy.
Erik Smith has to go. Absolutely has to.
Both Malone and Folk can be improved upon.
All of this needs looked at:
TL;DR Team needs:
The entire coaching/management regime basically
QB, RB, WR, WR, TE, DE, DT/NG, OLB, OLB, MLB, DB, S, K, P