This stuff is becoming all too common. I guess the word has gotten out about how to steal them and the break-in on the doors is very easy. You DO need a set of jimmijammers, I got them for all 4 doors, they were easy to install, total time about an hour. They DO make outside access via the door handles virtually impossible. I got the Ravelco installed a couple weeks ago, I can see what makes hot-wiring next to impossible as several parts of the ignition, fuel, and other stuff is safed from someone just splicing into wiring and bypassing the ignition. The most that will happen is that the thief will blow some fuses, but they certainly will not be driving your truck off. Today, I picked up the security module that Dodge sells for the Security Key the 2006/2007 model trucks use. I am installing that also. The 2006 and up trucks come with a RKE Keyfob - black key with all in one key/lock/unlock/panic, they no longer have a gray or black key difference, the key has the chip built in. The security module is P/N 1-82210637, it is specifically for the RKE Keyfob. It is called EVS Security. The unit was $159. out the door tax included. Comes with an installation manual, operators manual, nicely put together. Looks to be about a 2hour, easy install. With this unit you will have a fully-functional security/alarm system/security key system. I am sure that Dodge offers this for earlier model trucks also as the parts guy had to go through several items listed to get to my model.
Sorry to hear your truck was stolen, it may or may not be good that it was recovered, but you will take less of a beating insurance wise since you are not eating depreciation, etc probably just your deductable. Your toolbox should be covered, because it was bolted to the truck, that is considered permanent like any other bolted on part. Since you do not have your receipt, go to whomever you will buy a replacement box from, tell them your receipt problem, and have them write you one back dated to the purchase time and guarantee them you will be back to purchase a new toolbox from them. If need be, buy one on the spot as long as they will give you what you need receipt wise to help you out. If you know where your girlfriend bought yours from, go there to them for a receipt, and of course go back to them to purchase a toolbox.
As far as your tools or items stolen, if your box was locked, either your truck insurance or your homeowners insurance will cover them. Again, you will need receipts or proof that the items being claimed were in the toolbox. I take photos of this stuff and put them with my receipts. I also know that some insurance companies will take a written statement from someone other than yourself who witnessed these things being in the toolbox, sometimes all is not lost if your company is willing to take care of you. I had a toolbox broken into years ago, I had been with my company for a long time, my agent took a written statement as I did not keep good records then. Now my records are impeckable and kept in a safe place just in case.
A good body shop will fix your doors, be picky as to who you choose, and demand that your parts replacements are OEM, fight for this if need be. You began with OEM parts you should have OEM replacements. It is the aftermarket copy-cats that do not fit right or are slightly different from OEM that make the doors come out mis-aligned. I have a friend who does body work and he prefers OEM, in fact he has the customer sigh a waiver if the parts are not OEM because he has had so many problems with the copy-cats.
Good luck, and I hope you get it all resolved to you satisfaction. I would not sign anything until ALL the repair work is complete. I would also have more than one adjuster or shop price it out. You can go over the shop diagrams and come up with a meticulous list of parts needed and compare that to your estimates. This is no different - be an educated consumer. I would also have something in writing regarding a timeframe to drive and test out the mechanical stuff, say 90 days following return of your truck to have mechanical repairs made if you in fact have problems. That would be a reasonable amount of time to be sure all is correctly working. You might get some real balking about 90 days, but get some time until final closure of your claim out of them. When it is all over, consider getting MORE security stuff like I and others are doing. It will not necessarily stop your truck from being stolen again, but most thieves look for easy targets, all that you may add will increase the level of theft difficulty and make them think twice. It may be that they move on to someone elses truck or give up on that parking lot that night. The more we all do to have increased security to prevent theft, the more we all complicate the theft process after a while the thieves will not bother with our models BECAUSE we all are taking this stance with added security to deter them.
Again, good luck, please follow-up with this so everyone can benefit from your experience. It may very well be that your info will help others if/when the have to experience this unfortunate situation. Thanks for letting us all know what' going on.
CD
Attention: TDR Forum Junkies 
