Why not introduce some major incident that lets your PCs go unwatched, thus with the ability to free themselves and then help fight the incident?
Considering the fact that this is an historical campaign, you could start something big that didn't make it to the history books, and it could be thanks to your PC.
This way, your PC redeem themselves, AND write history!
The incident can even be Bob's character's doing, this way your PC:
- mess with history,
- fix it,
- stop Bob's character and may even kill him, to their great satisfaction,
- don't have the feeling that you saved them, in fact if you play this well, your only part will be to give them a chance to escape.
If you are concerned about how Bob will react, consider that you had a long talk with him, and he had several chances to correct his behavior. Clearly he had no respect for others' fun, so why bother?
This isn't a rules problem, it's a diva problem.
A player who wants the attention of the game focused on him and his awesomeness - by using attacks that let him dominate the battlefield and prevent other players from participating, or by getting upset and hogging your attention (via arguing about the rules) when he can't do so - is a diva, and needs to be handled as such.
Before doing anything, though, you need to determine how much his spotlight-hogging is bothering the other players. Do they get frustrated when he dominates combat and prevents them from joining in? Or are they happy to sit back and let him kill monsters, while they handle other things?
If everyone except you is generally happy with the status quo, then it's probably best to just let it go, and take that into account when building encounters. Give lots of mooks for the wizard to spam with Chain Lightning during combat, then give the other players spotlight time by including whatever type of scenario they enjoy. Let the wizard have his awesome. (Although if you don't enjoy this, then consider winding down the game and starting a new one that better suits your own style.)
Otherwise, assuming the other players also don't enjoy the wizard's behavior, you have a few options:
Enforce Your DM Authority
You're the DM, and you've already used that authority (however accidentally) to create houserules that benefit the players. Now use your authority to enforce houserules that don't benefit the players. When the wizard complains about a ruling you've made, say, "This game uses a lot of houserules. This is one of those houserules. Because of that, the rule you're citing doesn't apply in this case." As others have suggested, it may help to write down all your houserules explicitly, so that when the wizard tries to argue RAW, you can point to a specific houserule if applicable.
This is a socially tricky option, since it's likely to make the problem player feel punished. However, as long as you're consistent, polite, and firm, any tantrums he throws will reflect badly on him rather than you.
Reset the Rules
You say you have a bunch of houserules that mostly happened because you as a new DM didn't know any better, yet your wizard is trying to fight you with RAW. Explain to your players that keeping track of all your accidental houserules is becoming a problem, especially as the PCs increase in level and the math to balance things gets trickier. Then declare all house rules null and void, and require that play operates strictly on RAW from now on.
This option may be technically tricky, depending on the specific nature of your houserules. It may require reworking characters who've been built around the assumptions in the houserules. You may upset some of your other players who've been benefitting from the power-ups the houserules provide. And you'll almost certainly upset the wizard, who from your description will probably feel like he's being nerfed. However, you can point out - without naming names - that since your group is spending a lot of time during game going over the RAW, making sure all the PCs conform to the RAW will reduce that non-game time and let you spend more time actually playing.
Boot the Wizard
If the wizard's arguing is making the game not fun for you and the other players, but everyone else gets along just fine with each other and your houserules, then it may be best to simply stop playing with him. The easiest way to do this is to speak with the wizard privately. Tell him that you've come to realize that his playstyle is very different than that of the game you're running. Explain that this difference is making the game not fun for you (and if you know that other players don't enjoy his arguing, you can add "and others in the group", but absolutely don't name names). Tell him his character will be dealt with respectfully in game, and (if it's true) say that you'd be happy to game again with him sometime in the future, in a setting more compatible with both your playstyles.
This is another socially tricky option, but if this player is sapping all your game time arguing with you about the rules and hogging the spotlight, then it may be better for everyone to cut him loose.
Nuke the Game and Start Over
This is, well, the nuclear option: wrap up your game (could be as simple as "rocks fall everyone dies", or take a session or two to provide closure), then start a new game that either doesn't use houserules, or which has explicit agreement from all players that houserules will be used, and only minimal game time will be given to debating them (e.g., when dealing with a corner case). You can choose whether or not to invite the wizard back to this new game; if you think he'll continue to argue with you and hog the spotlight, it might be best - for your own sanity - to not continue to game with him.
Best Answer
I suspect that there is an underlying issue here which has little or nothing to do with the rules. He's not "lawyering" in the usual sense - probing the DM to see what loopholes he can exploit. What I gather from the description is that he's second-guessing the DM with regards to how difficult the encounter is.
Personally, I would do two things. First of all, I would have a discussion with your players about allowing DM creativity. For most of us DMs, a huge part of the fun of DMing is being able to create encounters, plots and schemes using this wonderful medium. When the players start second-guessing the DM over such details, it takes away from your fun. You had fun creating that encounter and hoped that it would be a source of fun for the players, too. The kvetching worked against that. Be clear on this: DM's should get to have fun.
Second, I would talk to that player about what was the real trigger there. Is it really that he views D&D as an entirely closed gaming system and any deviation from the canon is bad-wrong-fun? Was he worried about a potential TPK and thought that you were expressing a mean streak? Or perhaps he's a frustrated DM himself and can't help but put himself "behind the DM screen"? He might not know himself, but hopefully you can tease that bit of information out of him. If it's the first item, then continue that discussion about creativity. If it's the second, then he'll probably get over it after you play for a while and he gets used to your style. If it's the third, you might find ways to involve him in your DMing - perhaps he can design your next big boss encounter for you, or you can busy him by arranging for the party to obtain a stronghold which he needs to populate with guards and traps.
TL;DR: Talk it out. Express why this incident bothered you, establish the parameters for your own fun, find out what bothered him, and take his concerns into account in future games.