I'm going to disagree with you on a few things...
1) You can get a LOT of performance gains with a little bit of engine work. Headers, intake, cam, head work and exhaust can get you upwards of 150+ HP and 150+ TQ. It may be a little bit pricey but they are easy things to do one part at a time.
2) You cannot chip our ECU's, nor is there anyone who will reprogram them. The ONLY options for an ecu upgrade for us is an aftermarket ECU such as megasquirt. Using an aftermarket ECU you can reprogram your fuel map, timing, injector pulse, ect... You simply cannot modify our stock ecu's. You can sometimes do a few things to "trick" the ECU such as adjusting the AFM to make the ECU think that the motor is getting less or more air than it actually is.
3) You say to not look for large gains from a particular combination? Companies make combination kits with components that work VERY well together to make massive performance gains. IE: LCE Performance. They make an EFI top end kit that includes a big more throttle body, bored intake and injectors. That kit alone adds up to 15HP on a stock motor. That is better more than 10% increase in power to a stock motor. That's pretty good for our little underpowered motors. My motor for example, I have a LCE header, Street RV head, 268 cam, cylinders bored .030 over, deck milled .015, stock air filter housing delete with a high flow cone filter, under drive pulley (being installed tomorrow), and the A/C deleted. I have yet to dyno it but a lot of smart people on these motors (LCE, Engnbldr) have told me I'm upwards of around 155-160 HP and about 180TQ. That is a HUGE increase in power over stock on relatively small upgrades.
OP: Do some research and see for yourself that these little motors aren't too hard nor extremely expensive to upgrade and make more powerful.