Matt, I am assuming your in the USA. All vehicles sold in the US from 1996 on have an On-Board Diagnostic System required by Fed. Law with a unversal plug under the drivers side dashboard. You need to to have someone with a diagnostic code reader run a scan on your systems at this point. You can also rent them or buy one and do the diagnostics yourself. It sounds like mutiple things are going on and the only way to sort them out is to read the trouble codes stored in the diagnostic system....it will at least get you pointed in the right direction.
Good luck!
Cheers

__________________
FRED

Daily Driver: 98 E300TD 199K
Hobby Car: 69 Austin Mini
Past Diesels: 84 300SD, 312K
87 300SDL, 251K
94 Chev. K-1500 6.5Ltr.TD, 373K