A few thoughts. If money is limited, I would condsider limiting the amount of mechanical work to what is needed right now.
If it wasn't burning any oil it doesn't sound to me like it needs a rebore yet. They are pretty mechanically noisy, something which is magnified if like mine, someone has removed all the rubber fin packing pieces.
Whilst I'd agree that there is a high probability that 5th gear has some wear, if it wasn't noisy and you don't have to pull it apart for any other reason I'd put that down the priority list. If you decide to do it yourself, you need a 10 ton press and a good quality bearing puller or similar to exert pressure under the gear to pop it off.
You can remove the barrel and head in one piece to do the base gasket - saves replacing a good head gasket. Just be very careful reseating the cam chain guides.
I wouldn't change the oil pump as a matter of course, only if it doesn't measure up to the wear limits or is obviously scored etc.
If the small end is worn (and make sure it's not the gudgeon pin if there's play - it was on mine), in situ reaming and bushing (see Steve's advice above) sounds like a sensible option as long as you are not trying to build a high revving performance motor.
The cases on mine split and went together again very easily without needing any of the pullers (the ones for splitting/reasembling the cases that is) listed in the manual. It was a 40C day though so I'd suggest turning up the heating while you do those bits if you don't farm out that part. Yours might need the pullers etc, mine may have been an abberation.
Since the 1JK has an oil cooler as standard, I wouldn't worry about a tad more compression if you do want to change the piston. If the cam needs changed for other reasons (wear/scoring), getting a nice one designed to match a HC piston can cost less than standard bits and provide a sweeter motor than stock. Mine runs 11.5:1 with a specifically designed long duration cam and kicks nice and easy. Absolutely nothing wrong with leaving everything standard though.
If you need a new drive chain, buy a recognised brand name. Singles don't put out much HP, but they absolutely trash cheap chains.
Have fun, and don't get discouraged when it's all in bits and it starts to feel all too much. Every rebuild I've ever done has got to that stage at one point or another.