You will get no advantage from the 5 speed over the 4 except having to change an extra gear.  The ratios in high the same.  And, like others have said, the rest of that engine is real suspect.  It may have some serious hidden damage that you would find splitting the case.

As far as the title.  I would keep the bill of sale, title, etc., not title it unless I wanted to use the frame to make a rider of some sort or sell the frame to someone who wanted to license the bike they built with it.  If you have all of the paperwork to prove that it's yours, you can sell it to someone else without ever having the title in your name.  

Your state may have some law that requires you to title in x number of days of purchase whether or not you intend to license and ride it.  If so, there's a way to get title only without worrying about plates and stuff.  If you have a law like this and don't title within the allotted time, you might be subject to a big late fee when you try to transfer it to someone else or license it yourself.

Thanks for input folks.

Today I called DOL and they told me that since I've got title I need to register bike. I'll talk to them during visit to understand better situation, but looks like in Washington state there is not much choice.

This leaves me with 2 options:

1. Take off all nice shiny parts from 2003 and install them on rusty 1986 (including starter stuff).
2. Install starter stuff on 1986 engine and install engine on 2003.

Since 1986 runs just fine now I hate to "fix what is not broken". But may be I'm missing something, any thoughts would be highly appreciated.

Answering justin_o_guy2 question: I paid $50. After that I paid $80 for uhaul cargo van. And looks like I'll pay something to DOL. Nevertheless I think this was unbelievable deal.

Thanks Verslagen, but may I ask you to clarify what "non-op" means here? Mark it as non operational? In case I'll decide to put 1986 engine to 2003 bike would I be able to mark it operational again?

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I have a low miles '86 engine in a 2005 frame. In AZ I believe the frame is titled but the engine is not so you can swap motors all day long in your frame with a title.

I took off engine from the bike and got alternator cover off. From my point of view it makes sense to swap starter gear and cover so I'll not have to drill the old cover.

What bothers me is that after removing cover I found part of piston and filings. What do you think, would it be safe to wash cover with coils and install it?

Thanks Verslagen! No shorts found, each coil is 0.21 ohms, looks good. I'll wash out all trash and would try to install it in the nearest future.

Kirill.....or any others that have both a 4 and 5 speed.

Next time you have the clutch cover off either or both of the engines, count the teeth on the crankshaft gear and clutch gear of the 4 and 5 speed engines....and see if they are the same.  If they are different it might be a way to alter the gearing a bit.

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that's pretty much it.