This definitely more an infrastructure question -- specific to your organization's workflow, internal policies, existing software, priorities and politics -- than a general 'where do I implement {kerberos, RSA SecurID, off-site audit trails, etc}. You won't get a one-size fits all solution, as it totally depends on 1) the industry you're working in, 2) the internal compliance policies you have to deal with, 3) the country you're operating in, 4) the operating policies you have to follow in order to stay compliant with the clients professional liability insurance policy/policies.

>> "lots change as you try to build a complete system"
I mean this is why in the enterprise, changing one line of code can take 2 weeks of conference calls (in-house legal often has to be brought in, the original stakeholder of the project has to be brought in and odds are he's gone so whoever inherited the project has to be brought in, if you're making a fundamental change to the system often third-party auditors from the big 4 are requested to sign-off on the logistics of the change (especially if you're a publically traded company operating within the US).

RE: Purchase ordering systems - this has been standardized via multiple standards, but most of the companies I've consulted with have one integrated system (usually SAP, Dynamics, or one of the other handful of big-name brands), and they all speak the EDI standard[1], or if not, you'll certainly have Connector modules. I.e., BizTalk (if you're on a MS Dynamics stack, that's what you'll be using for workflow) has a SAP connector, SAP has a connector for Epicor, etc. With respect to security in terms of server<->server PO negotiation, read this[2] if you're on the MS stack. SAP R/3,4 (and B1, and AIO) all take care of the issuing of the PO, validating incoming POs (i.e., the SAP FSCM module will take care of customer management to see if the credit line is available for the customer, and all that; the FI/CO stuff will take care of balancing the accounting journals); the workflows [defined within BizTalk for MS or using custom ABAP modules that were placed in during your SAP implementation], the security negotiation is usually done via AS2 (see: [2]) or through one of a few 3rd party EDI transaction entities (in the same way that there are like 4 major CC companies, like-so with those EDI value-added transactors). x.509 and ActiveDirectory are almost always the standard re: authentication[3]

CRM's are historically purchased as a module that plugs into your ERP.

Lemur and Let's Encrypt have _nothing_ to do with anything enterprise and belong nowhere near it. (The fact that you even posed this question makes me really concerned) LE is great for the average Joe developer because it democratized SSL cert generation, but even if a VeriSign SSL is 100$ that's, what? half an hour of a consultants time? My clients get that warm feeling every time they see a brand-name as a line-item on their invoice. Managers are all about mitigating risk. This is why you have VMware instances running 30 year old software simulating DEC Alphas, and why consultants who have skillsets in REXX and JCL can bill higher than associates in BigLaw. Any project has risk attached to it, an integration/re-write project has avoidable risk. Delegate the risk factor out by getting the CIO to sign off on a restructuring program that's done by consultants so if it fails you can blame Accenture or IBM Consulting. I would never, ever take on a project like that, even at triple my rate, because it sounds like you're already entrenched in a fractured system and in my experience those projects fail. I never take any work that I'm 100% sure I can complete because one major mess up and my reputation is shot. And this is the type of integration I do for a living. [Read this if you take nothing else away from my advice - [4]].

Even if you can write a 30 line Ruby script that integrates all of your systems into one magical, fluid operation, if there's even a slight chance of failure, you will be the one who assumes responsibility. Furthermore, 6 months down the line when middle-management and/or upper management is evaluating your performance, this is what they'll remember.

Your company is an enterprise. You have a fractured knowledge base with 'wildly different authentication [schemes]'. Bring in consultants and don't risk your career.

[1] https://en.wikipedia.org/wiki/X12_Document_List Enjoy spending the next 2 years reading.
[2] https://msdn.microsoft.com/en-us/library/bb743507.aspx
[3] Here it is in SAP Netweaver (not to be confused with R/3, the actual SAP) - it's fairly similar though in the methodology though as is any of the other ERP / CRM's. http://help.sap.com/saphelp_nw70/helpdata/EN/d3/1dd4516c5186...
[4] https://news.ycombinator.com/item?id=10639309 Read my post here on why rolling your own solution is bad for your customer, and even worse for you.