Hi MissingMyDad - MMD.
What deep and mixed emotions this entire thread brings out in one. I, too, am most sorry to learn of your heartache; very glad you've found a network community here at W/S (fantastic posts, ideas, support) yet quite troubled LE seem to be keeping you at arm's length. The latter perhaps one of the toughest daily milestones to endure. Here's trusting the task force will bear fruit and indeed lessen your load. Thoughts and prayers to you.
Meantime ... here are my thoughts FWIW, indeed others have commented along similar lines - sorry if it's too long - just another theory:
You've told us (endorsed by locals in the press), what a kind, giving and caring person your father was (bless him). This in and of itself made him a 'sought-after target'. Word gets out that "Joe Neff bailed me out; feeds us free on Sundays - carries/deals with a lot of cash and is retiring soon". All of those actions translate into "great opportunity for money" to more desperate, cunning folk.
We're also told from the get-go, LE claimed "this was personal"...
You then wrote something quite poignant - very early on - regarding the (good) advice your dad gave you:
"Don't ever lend more than you're willing to give away...".
Do you / LE / anyone know all the people - from family onwards - that your dad helped out? Within that group of very fortunate souls - there may be one or more whom your father decided he was not prepared to give any more?
That/those person/s may have known your father's footsteps and habits; known the best time to approach him; known his 'cash-run' timings and therefore it may very well have been your own father who took the 'missing thousands' from the safe - not for the life of him believing he'd be murdered - he left the safe door open as he may easily have done previously if in a rush, then locked the internal door - and left.
However, when he reached the bar - he may have allowed a familiar face to come in (he knew him, felt safe, if not in control) whom he'd helped before. When he said no - he may have been literally taken by surprise & side-swiped. A bloody fight ensued and the 'thousands' he himself may have taken from the safe could have been stolen . He may have been shot so as not to identify the perp and bundled into another vehicle. He could have been taped up semi-conscious so as not to arouse suspicion; the perp may not have been convinced he was dead or - to stop him defending himself.
The perp may not even have known about the $740 in his top pocket... but took his cigarettes (agree with previous poster - he's possibly a smoker) cell phone and keys. He's definitely local, definitely knew your dad - probably even went to the funeral. Are there any tapes of the funeral? Would you (and those close to Joe), all this time later, be able to identify those he'd helped out? Maybe this person would have wanted no waves; just blend in and be a part of a bigger crowd...
If you haven't seen the ME report - you wont know if there was water on his lungs (very sorry to be graphic - I'm just spelling out my thoughts. If this info has been identified, sorry - 20 plus pages is a lot to remember...).
Greed, sex, drugs, rock n roll and alcohol are key reasons for murder. The ghastly final act being of revenge ---> no witnesses & utter paranoia.
Ramble over. Many blessings. This WILL unravel; stay strong and focused, MMD.
PSA