Does this imply that you are using IDE drives? If so, you might also have to change the boot order in the BIOS after changing the jumper settings. I have cloned a 250 G drive onto a 640 G drive using clonezilla before, so the different capacities shouldn't be the problem.
Let's get names and functions straight, because I've seen people cause themselves trouble trying to do it wrong.
The terms "Master" and "Slave" are relevant ONLY to IDE drive systems. One IDE port and cable can always support TWO drive units. Hence the design makes it necessary to mark each unit differently somehow, and that system is the Master / Slave system. Jumpers on pins on the drive unit are used for this. Any IDE port MUST have a Master unit. IF there is a second unit on the port / cable, then it MUST be the Slave. The only exception to this is that you can set BOTH units to the "CS" jumper setting (for Cable Select), and then the unit on the END connector of the cable will be the Master.
If you have two IDE ports and cables, EACH are subject to those rules. That is, EACH port (if it is used) MUST have a Master, and MAY have a Slave also.
In SATA drive systems there are NO Master or Slave settings, because a SATA port only handles ONE device. Now, many SATA HDD units DO have pins on the back edge and a jumper or two, but these are NOT to be used for Master or Slave. ONE such jumper is commonly used in Seagate and WD drives (and probably others) to force a drive to slow down to the original 1.5 Gb/s communication speed of the first version of SATA. Usually if you know you have SATA II controllers in your machine you should remove that jumper. On WD HDD's (maybe others) you can install a jumper on a particular other pin pair to force it to what is called PM2 or PUIS mode. When this is done, the drive will initiate but will NOT spin up ready to use, and it waits for an order to spin up. This in ONLY used with some RAID controllers in servers that minimize disk rotation when not in use. Most computer controllers will NOT issue the spin-up command, so a drive set this way will appear to be DEAD! So, moral of the story: do NOT change jumpers on a SATA drive unless you KNOW what you are doing. Check the manufacturer's website if in doubt.
There is no such thing as a Master drive for a computer. In former times it was very common for the Master device on the Primary IDE port to be, by default, the Boot Drive. But for at least a decade now the choice of Boot Drive has been established separately. Within BIOS Setup there is a place where you set the Boot Priority Sequence. Many people set this to try the optical drive first, then a specific hard drive unit (IDE Master or Slave, or SATA, depends on where you installed your OS), and often no other choices. (My own sequence is the floppy drive first (yes, I have one), the first (of two) DVD burners, and then the first (of two) SATA HDD's.) Others have bootable flash drives on USB2 ports as one option.
So, OP, first point is, as said by others, are you actually using IDE drives? If you are, then make sure the Master and Slave settings are correct. If two IDE drives are on one cable, they must be different. However, if you have two IDE drives on DIFFERENT cables and ports, probably each needs to be Master of its own port. If both your drives are IDE units on the same port and cable and both are set to "CS", then the unit plugged into the END connector will be that port's Master.
On the other hand, IF you are using SATA drives, you should NOT have been juggling jumpers. In this situation I recommend you go to the manufacturer's websites for the drives and find the correct original jumper settings and restore them. IF you know you have SATA II controllers you may want to remove the jumpers entirely on your SATA units - again, check the websites.
Now, with jumpers set properly, use the BIOS Setup screen for Boot Priority Sequence to set the new larger drive (wherever it is connected, and remember that you CAN chose an IDE Master, an IDE Slave OR a SATA device to boot from) as the Boot Device, and make sure the older drive is NOT in this list.
Let me ad one minor note. On any IDE port / cable if you have both a hard drive and an optical drive on that port, it is recommended that the HARD DRIVE should be the MASTER. In some earlier pieces of hardware, optical drives had difficulty filling the Master function when paired with a hard drive as Slave. So this guideline is a precaution for those situations.