This question might be answered in one simple reply.

2000 Dyna Super Glide TC88, 5 speed box and it feels as though the gearbox may be on the way out, clutch burning smell is one sympton I can detect but also gearbox is selecting neutral in between 3rd and 4th and sometimes on the way back down between 4th and 3rd, sometimes (although rarely) between 3rd and 2nd. I also cannot get it in into neutral if, for intance, I am sitting at the lights and then want to select neutral, it can only be done when slowing down to a stop then just before pulling up it has to be in first then changed into neutral.

I will be reluctantly offloading the bike around September so keeping that in mind what is the best option?

At least with the extra money from the "reluctant" sale, you will cover the expense of any transmission repair.

Experiencing difficulty in selecting neutral does not primarily indicate a gearbox issue. Though it could be, it is far more likely to be a clutch adjustment matter. Do you have a genuine cable?
A burning clutch smell is in not really a symptom of any gearbox issue, unless, of course, the transmission was completely seized, and you were trying to take off.
Is there any oil in the primary?

It will always be more difficult to find neutral from 2nd, as the ramps on the shifter drum are designed that way... to avoid hitting neutral from second.

Seeing as you are (hoping to be) selling the bike in september, and that you would never ever sell anything defective to another enthusiast, you will be wanting to repair the bike properly.
It is very common for the dogs on the gears to wear, and the only proper fix for this is to replace the worn parts. Exactly what is happening inside the trans will not be fully known until dis-assembly and inspection, but it is likely you will need at least 2 gears, and possibly more, as well as various other items(gaskets, possibly bearings, etc). The shifter return spring is a known weakness, and I would recommend replacing with a new genuine item, whether it looks bad or not.

I think I would start with a clutch cable service and adjustment, and if there was no improvement anywhere, proceed with further work.

Repair or replace? 5 speeds are always repaired unless there is major case damage.

Thanks DR. Changed all the oils ('cept fork) around 2000k's ago and checked again recently, all levels are good. Also had 14" ape's installed by an indie whereby they replaced all clutch cables but come to think of it there is no freeplay with the clutch, not even a mm.

I guess as usual start with the cheap shit then maybe work my way up.

 There's a manual for download here to suit your model.

 

http://www.4shared.com/account/dir/mWghPw7P/sharing.html

Another thing I left out is sometimes in first when moving off from the lights (no clutching involved) it skips a bit in first. The cable itself is also very tight as in it doesn't have much slack, it goes straight out the lever and down to the frame then to the gearbox.

Thanks guys, have a manual so I'll have a play on the weekend and see how it goes. Have a feeling I need a longer cable though.

adjust your cable first, either at the cable,or if you have no adjustment there, then at the clutch itself. burning clutch smell usually indicates clutch is slipping or riding. a riding clutch can cause some of the symptoms you described.

Alrighty, had the cable adjusted and all seems to be going well. It can easily select neutral now and doesn't want to take off when sitting at the lights in first. Plenty of freeplay but can one have too much freeplay?

The clutch lever is so far out that the tops of my finger are what's used to pull the lever in and as soon as I touch the lever, I need only move it a couple of centimeters (if that) for it to change gear. Also now when I give it a fist full in 3rd, 4th or 5th it is over-revving like the clutch is slipping which never happened prior to the clutch adjustment.

So I guess the question is, can there be too much freeplay?

Might have to buy a proper manual, mine has everything in it about clutch and primary drive assemblies but nothing about adjusting the cable itself.

 

Anyway had the clutch cable played with today (by a pro) and 4th and 5th gears are slipping so may need a rebuild I'm thinking.

After running out on the bike to the Harley drags today there was no slipping. I think it was a figment of my imagination and as Angry alluded to, the clutch was over adjusted causing slipping and now it seems to have settled after being re-adjusted.

Thanks everyone for your help.